2′-branched nucleosides and Flaviviridae mutation

ABSTRACT

The present invention discloses a method for the treatment of Flaviviridae infection that includes the administration of a 2′-branched nucleoside, or a pharmaceutically acceptable prodrug and/or salt thereof, to a human in need of therapy in combination or alternation with a drug that directly or indirectly induces a mutation in the viral genome at a location other than a mutation of a nucleotide that results in a change from serine to a different amino acid in the highly conserved consensus sequence, XRX S GXXXT (SEQ ID NO: 63), of domain B of the RNA polymerase region, or is associated with such a mutation. The invention also includes a method to detect a mutant strain of Flaviviridae and a method for its treatment.

CROSS-REFERENCE

This application is a continuation of U.S. application Ser. No.10/715,729, filed on Nov. 17, 2003, now issued as U.S. Pat. No.7,824,854, which claims priority to U.S. Provisional Application No.60/426,675, filed on Nov. 15, 2002, the disclosures of which are herebyincorporated by reference in their entireties.

SEQUENCE LISTING

Filed with the present specification is a computer readable form (CRF)copy of the Sequence Listing. The CRF entitled “11874-245-999sequence.txt” was created on Jan. 14, 2011 and is 12,451 bytes in size,is identical to the paper copy of the Sequence Listing, and isincorporated herein by reference in its entirety.

FIELD OF THE INVENTION

This invention is a method for the treatment of Flaviviridae infectionin a host, such as a human, in need of such therapy, that includes theadministration of a 2′-branched nucleoside, or a pharmaceuticallyacceptable salt, ester, or prodrug thereof, in combination and/oralternation with one or more drugs that directly or indirectly induce amutation in a Flaviviridae at a location other than a mutation of anucleotide that results in a change from serine to a different aminoacid in the highly conserved consensus sequence, XRXSGXXXT (SEQ ID NO:63), of domain B of the RNA polymerase region, and/or one or more drugsthat are associated with such a mutation. The invention also includes amethod for the treatment of Flaviviridae infection in a host, such as ahuman, in need of such therapy, that includes the administration of a2′-branched nucleoside, or a pharmaceutically acceptable salt, ester, orprodrug thereof, in combination and/or alternation with interferon. Theinvention also includes a method to detect a mutant strain ofFlaviviridae and a method for its treatment, and kits and materials forsuch detection.

BACKGROUND OF THE INVENTION

The Flaviviridae family of viruses comprises at least three distinctgenera: pestiviruses, which cause disease in cattle and pigs;flaviviruses, which are the primary cause of diseases such as denguefever and yellow fever; and hepaciviruses, whose sole member is HCV. Theflavivirus genus includes more than 68 members separated into groups onthe basis of serological relatedness (Calisher et al., J. Gen. Virol,1993, 70, 37-43). Clinical symptoms vary and include fever, encephalitisand hemorrhagic fever (Fields Virology, Editors: Fields, B. N., Knipe,D. M., and Howley, P. M., Lippincott-Raven Publishers, Philadelphia,Pa., 1996, Chapter 31, 931-959). Flaviviruses of global concern that areassociated with human disease include the dengue hemorrhagic feverviruses (DHF), yellow fever virus, West Nile virus, shock syndrome andJapanese encephalitis virus (Halstead, S. B., Rev. Infect. Dis., 1984,6, 251-264; Halstead, S. B., Science, 239:476-481, 1988; Monath, T. P.,New Eng. J. Med., 1988, 319, 641-643).

The pestivirus genus includes bovine viral diarrhea virus (BVDV),classical swine fever virus (CSFV, also called hog cholera virus) andborder disease virus (BDV) of sheep (Moennig, V. et al. Adv. Vir. Res.1992, 41, 53-98). Pestivirus infections of domesticated livestock(cattle, pigs and sheep) cause significant economic losses worldwide.BVDV causes mucosal disease in cattle and is of significant economicimportance to the livestock industry (Meyers, G. and Thiel, H.-J.,Advances in Virus Research, 1996, 47, 53-118; Moennig V., et al, Adv.Vir. Res. 1992, 41, 53-98). Human pestiviruses have not been asextensively characterized as the animal pestiviruses. However,serological surveys indicate considerable pestivirus exposure in humans.

Pestiviruses and hepaciviruses are closely related virus groups withinthe Flaviviridae family. Other closely related viruses in this familyinclude the GB virus A, GB virus A-like agents, GB virus-B and GBvirus-C (also called hepatitis G virus, HGV). The hepacivirus group(hepatitis C virus; HCV) consists of a number of closely related butgenotypically distinguishable viruses that infect humans. There areapproximately 6 HCV genotypes and more than 50 subtypes. HCV is a majorcause of hepatitis globally. Most HCV infections become persistent andabout 75% of cases develop chronic liver disease. Chronic HCV infectioncan lead to development of cirrhosis, hepatocellular carcinoma and liverfailure. Due to the similarities between pestiviruses and hepaciviruses,combined with the poor ability of hepaciviruses to grow efficiently incell culture, bovine viral diarrhea virus (BVDV) is often used as asurrogate to study the HCV virus.

The genetic organization of pestiviruses and hepaciviruses is verysimilar. These positive stranded RNA viruses possess a single large openreading frame (ORF) encoding all the viral proteins necessary for virusreplication. These proteins are expressed as a polyprotein that is co-and post-translationally processed by both cellular and virus-encodedproteinases to yield the mature viral proteins. The viral proteinsresponsible for the replication of the viral genome RNA are locatedwithin approximately the carboxy-terminal two-thirds of the ORF and aretermed nonstructural (NS) proteins. The genetic organization andpolyprotein processing of the nonstructural protein portion of the ORFfor pestiviruses and hepaciviruses is very similar. For both thepestiviruses and hepaciviruses, the mature nonstructural (NS) proteins,in sequential order from the amino-terminus of the nonstructural proteincoding region to the carboxy-terminus of the ORF, consist of p7, NS2,NS3, NS4A, NS4B, NS5A, and NS5B.

The NS proteins of pestiviruses and hepaciviruses share sequence domainsthat are characteristic of specific protein functions. For example, theNS3 proteins of viruses in both groups possess amino acid sequencemotifs characteristic of serine proteinases and of helicases (Gorbalenyaet al. (1988) Nature 333:22; Bazan and Fletterick (1989) Virology171:637-639; Gorbalenya et al. (1989) Nucleic Acid Res. 17.3889-3897).Similarly, the NS5B proteins of pestiviruses and hepaciviruses have themotifs characteristic of RNA-directed RNA polymerases (Koonin, E. V. andDolja, V. V. (1993) Crit. Rev. Biochem. Molec. Biol. 28:375-430).

Furthermore, the actual roles and functions of the NS proteins ofpestiviruses and hepaciviruses in the lifecycle of the viruses aredirectly analogous. In both cases, the NS3 serine proteinase isresponsible for all proteolytic processing of polyprotein precursorsdownstream of its position in the ORF (Wiskerchen and Collett (1991)Virology 184:341-350; Bartenschlager et al. (1993) J. Virol.67:3835-3844; Eckart et al. (1993) Biochem. Biophys. Res. Comm.192:399-406; Grakoui et al. (1993) J. Virol. 67:2832-2843; Grakoui etal. (1993) Proc. Natl. Acad. Sci. USA 90:10583-10587; Hijikata et al.(1993) J. Virol. 67:4665-4675; Tome et al. (1993) J. Virol.67:4017-4026). The NS4A protein, in both cases, acts as a cofactor withthe NS3 serine protease (Bartenschlager et al. (1994) J. Virol.68:5045-5055; Failla et al. (1994) J. Virol. 68: 3753-3760; Lin et al.(1994) 68:8147-8157; Xu et al. (1997) J. Virol. 71:5312-5322). The NS3protein of both viruses also functions as a helicase (Kim et al. (1995)Biochem. Biophys. Res. Comm. 215: 160-166; Jin and Peterson (1995) Arch.Biochem. Biophys., 323:47-53; Warrener and Collett (1995) J. Virol.69:1720-1726). Finally, the NS5B proteins of pestiviruses andhepaciviruses have the predicted RNA-directed RNA polymerases activity(Behrens et al. (1996) EMBO J. 15:12-22; Lchmann et al. (1997) J. Virol.71:8416-8428; Yuan et al. (1997) Biochem. Biophys. Res. Comm.232:231-235; Hagedorn, PCT WO 97/12033; Zhong et al. (1998) J. Virol.72.9365-9369).

Examples of antiviral agents that have been identified as active againstthe Flaviviridae family of viruses include:

(1) Interferon

Interferons (IFNs) are compounds that have been commercially availablefor the treatment of chronic hepatitis for nearly a decade. IFNs areglycoproteins produced by immune cells in response to viral infection.IFNs inhibit viral replication of many viruses, including HCV, and whenused as the sole treatment for hepatitis C infection, IFN suppressesserum HCV-RNA to undetectable levels. Additionally, IFN normalizes serumamino transferase levels. Unfortunately, the effects of IFN aretemporary and a sustained response occurs in only 8%-9% of patientschronically infected with HCV (Gary L. Davis. Gastroenterology118:S104-S114, 2000).

A number of patents disclose HCV treatments using interferon-basedtherapies. For example, U.S. Pat. No. 5,980,884 to Blatt et al.discloses methods for retreatment of patients afflicted with HCV usingconsensus interferon. U.S. Pat. No. 5,942,223 to Bazer et al. disclosesan anti-HCV therapy using ovine or bovine interferon-tau. U.S. Pat. No.5,928,636 to Alber et al. discloses the combination therapy ofinterleukin-12 and interferon alpha for the treatment of infectiousdiseases including HCV. U.S. Pat. No. 5,908,621 to Glue et al. disclosesthe use of polyethylene glycol modified interferon for the treatment ofHCV. U.S. Pat. No. 5,849,696 to Chretien et al. discloses the use ofthymosins, alone or in combination with interferon, for treating HCV.U.S. Pat. No. 5,830,455 to Valtuena et al. discloses a combination HCVtherapy employing interferon and a free radical scavenger. U.S. Pat. No.5,738,845 to Imakawa discloses the use of human interferon tau proteinsfor treating HCV. Other interferon-based treatments for HCV aredisclosed in U.S. Pat. No. 5,676,942 to Testa et al., U.S. Pat. No.5,372,808 to Blatt et al., and U.S. Pat. No. 5,849,696.

(2) Ribavirin (Battaglia, A. M. et al., Ann. Pharmacother, 2000, 34,487-494); Berenguer, M. et al. Antivir. Ther., 1998, 3 (Suppl. 3),125-136).

Ribavirin (1-β-D-ribofuranosyl-1-1,2,4-triazole-3-carboxamide) is asynthetic, non-interferon-inducing, broad spectrum antiviral nucleosideanalog. It is sold under the trade names Virazole™ (The Merck Index,11th edition, Editor: Budavari, S., Merck & Co., Inc., Rahway, N.J., p1304, 1989); Rebetol (Schering Plough) and Co-Pegasus (Roche). U.S. Pat.No. 3,798,209 and RE29,835 (ICN Pharmaceuticals) disclose and claimribavirin. Ribavirin is structurally similar to guanosine, and has invitro activity against several DNA and RNA viruses includingFlaviviridae (Gary L. Davis. Gastroenterology 118:S104-S114, 2000). U.S.Pat. No. 4,211,771 (to ICN Pharmaceuticals) discloses the use ofribavirin as an antiviral agent. Ribavirin reduces serum aminotransferase levels to normal in 40% of patients, but it does not lowerserum levels of HCV-RNA (Gary L. Davis. Gastroenterology 118:S104-S114,2000). Thus, ribavirin alone is not effective in reducing viral RNAlevels. Additionally, ribavirin has significant toxicity and is known toinduce anemia.

Combination of Interferon and Ribavirin

Schering-Plough sells ribavirin as Rebetol® capsules (200 mg) foradministration to patients with HCV. The U.S. FDA has approved Rebetolcapsules to treat chronic HCV infection in combination with Schering'salpha interferon-2b products Intron® A and PEG-Intron™. Rebetol capsulesare not approved for monotherapy (i.e., administration independent ofIntron®A or PEG-Intron), although Intron A and PEG-Intron are approvedfor monotherapy (i.e., administration without ribavirin). Hoffman LaRoche is selling ribavirin under the name Co-Pegasus in Europe and theUnited States, also for use in combination with interferon for thetreatment of HCV. Other alpha interferon products include Roferon-A(Hoffmann-La Roche), Infergen® (Intermune, formerly Amgen's product),and Wellferon® (Wellcome Foundation) are currently FDA-approved for HCVmonotherapy. Interferon products currently in development for HCVinclude: Roferon-A (interferon alfa-2a) by Roche, PEGASYS (pegylatedinterferon alfa-2a) by Roche, INFERGEN (interferon alfacon-1) byInterMune, OMNIFERON (natural interferon) by Viragen, ALBUFERON by HumanGenome Sciences, REBIF (interferon beta-1a) by Ares-Serono, OmegaInterferon by BioMedicine, Oral Interferon Alpha by AmarilloBiosciences, and Interferon gamma-1b by InterMune.

The combination of IFN and ribavirin for the treatment of HCV infectionhas been reported to be effective in the treatment of IFN naïve patients(Battaglia, A. M. et al., Ann. Pharmacother. 34:487-494, 2000).Combination treatment is effective both before hepatitis develops andwhen histological disease is present (Berenguer, M. et al. Antivir.Ther. 3(Suppl. 3):125-136, 1998). Currently, the most effective therapyfor HCV is combination therapy of pegylated interferon with ribavirin(2002 NIH Consensus Development Conference on the Management ofHepatitis C). However, the side effects of combination therapy can besignificant and include hemolysis, flu-like symptoms, anemia, andfatigue (Gary L. Davis. Gastroenterology 118:S104-S114, 2000).

(3) Substrate-based NS3 protease inhibitors (for example, Attwood etal., Antiviral peptide derivatives, PCT WO 98/22496, 1998; Attwood etal., Antiviral Chemistry and Chemotherapy 1999, 10, 259-273; Attwood etal., Preparation and use of amino acid derivatives as anti-viral agents,German Patent Pub. DE 19914474; Tung et al. Inhibitors of serineproteases, particularly hepatitis C virus NS3 protease, PCT WO98/17679), including alphaketoamides and hydrazinoureas, and inhibitorsthat terminate in an electrophile such as a boronic acid or phosphonate(Llinas-Brunet et al, Hepatitis C inhibitor peptide analogues, PCT WO99/07734).

(4) Non-substrate-based inhibitors, for example,2,4,6-trihydroxy-3-nitro-benzamide derivatives (Sudo K. et al.,Biochemical and Biophysical Research Communications, 1997, 238, 643-647;Sudo K. et al. Antiviral Chemistry and Chemotherapy, 1998, 9, 186),including RD3-4082 and RD3-4078, the former substituted on the amidewith a 14 carbon chain and the latter processing a para-phenoxyphenylgroup;

(5) Thiazolidine derivatives which show relevant inhibition in areverse-phase HPLC assay with an NS3/4A fusion protein and NS5A/5Bsubstrate (for example Sudo K. et al., Antiviral Research, 1996, 32,9-18), especially compound RD-1-6250, possessing a fused cinnamoylmoiety substituted with a long alkyl chain, RD4 6205 and RD4 6193;

(6) Thiazolidines and benzanilides (for example Kakiuchi N. et al. J.EBS Letters 421, 217-220; and Takeshita N. et al. AnalyticalBiochemistry, 1997, 247, 242-246);

(7) A phenanthrenequinone possessing activity against protease in aSDS-PAGE and autoradiography assay isolated from the fermentationculture broth of Streptomyces sp., for example, Sch 68631 (Chu M. etal., Tetrahedron Letters, 1996, 37, 7229-7232), and Sch 351633, isolatedfrom the fungus Penicillium griscofuluum, which demonstrates activity ina scintillation proximity assay (Chu M. et al., Bioorganic and MedicinalChemistry Letters 9, 1949-1952);

(8) Selective NS3 inhibitors, for example, those based on themacromolecule elgin c, isolated from leech (Qasim M. A. et al.,Biochemistry, 1997, 36, 1598-1607);

(9) Helicase inhibitors (for example Diana G. D. et al., Compounds,compositions and methods for treatment of hepatitis C, U.S. Pat. No.5,633,358; Diana G. D. et al., Piperidine derivatives, pharmaceuticalcompositions thereof and their use in the treatment of hepatitis C, PCTWO 97/36554);

(10) Polymerase inhibitors for example nucleotide analogues, gliotoxin(Ferrari R. et al. Journal of Virology, 1999, 73, 1649-1654), and thenatural product cerulenin (Lohmann V. et al., Virology, 1998, 249,108-118);

(11) Antisense phosphorothioate oligodeoxynucleotides (S-ODN)complementary to sequence stretches in the 5′ non-coding region (NCR) ofthe virus (Alt M. et al., Hepatology, 1995, 22, 707-717), or nucleotides326-348 comprising the 3′ end of the NCR and nucleotides 371-388 locatedin the core coding region of the HCV RNA (Alt M. et al., Archives ofVirology, 1997, 142, 589-599; Galderisi U. et al., Journal of CellularPhysiology, 1999, 181, 251-257).

(12) Inhibitors of IRES-dependent translation (Ikeda N et al., Agent forthe prevention and treatment of hepatitis C, Japanese Patent Pub.JP-08268890; Kai Y. et al. Prevention and treatment of viral diseases,Japanese Patent Pub. JP-10101591).

(13) Nuclease-resistant ribozymes (for example Maccjak, D. J. et al.,Hepatology 1999, 30, abstract 995).

(14) Nucleoside analogs have also been developed for the treatment ofFlaviviridae infections.

Idenix Pharmaceuticals, Ltd. discloses branched nucleosides, and theiruse in the treatment of HCV and flaviviruses and pestiviruses in USPatent Publication No. 2003/0050229 A1 and US Patent Publication No.2003/0060400 A1, which correspond to International Publication Nos. WO01/90121 and WO 01/92282. A method for the treatment of hepatitis Cinfection (and flaviviruses and pestiviruses) in humans and other hostanimals is disclosed in the Idenix publications that includesadministering an effective amount of a biologically active 1′, 2′, 3′ or4′-branched β-D or β-L nucleosides or a pharmaceutically acceptable saltor prodrug thereof, administered either alone or in combination,optionally in a pharmaceutically acceptable carrier.

Other patent applications disclosing the use of certain nucleosideanalogs to treat hepatitis C virus include: International PatentPublication Nos. WO 01/32153 (PCT/CA00/01316; filed Nov. 3, 2000) and WO01/60315 (PCT/CA01/00197; filed Feb. 19, 2001) filed by BioChem Pharma,Inc. (now Shire Biochem, Inc.); US Patent Publication No. 2002/0147160and the corresponding International Patent Publication Nos. WO 02/057425(PCT/US02/01531; filed Jan. 18, 2002) and WO 02/057287 (PCT/US02/03086;filed Jan. 18, 2002) filed by Merck & Co., Inc.; US Patent PublicationNos. 2003/083307 A1 and US 2003/008841 A1, and the correspondingInternational Patent Publication Nos. WO 02/18404 (PCT/EP01/09633;published Aug. 21, 2001); WO 02/100415 and WO 02/094289, filed byHoffman-LaRoche; US Patent Publication No. 2003/028013 A1 and thecorresponding International Patent Publication Nos. WO 03/062255 and WO03/061385 filed by Ribapharm; and WO 01/79246 and WO 02/32920 filed byPharmasset.

(15) Miscellaneous compounds including 1-amino-alkylcyclohexanes (U.S.Pat. No. 6,034,134 to Gold et al.), alkyl lipids (U.S. Pat. No.5,922,757 to Chojkier et al.), vitamin E and other antioxidants (U.S.Pat. No. 5,922,757 to Chojkier et al.), squalene, amantadine, bile acids(U.S. Pat. No. 5,846,964 to Ozeki et al.),N-(phosphonoacetyl)-L-aspartic acid, (U.S. Pat. No. 5,830,905 to Dianaet al.), benzenedicarboxamides (U.S. Pat. No. 5,633,388 to Diana etal.), polyadenylic acid derivatives (U.S. Pat. No. 5,496,546 to Wang etal.), 2′,3′-dideoxyinosine (U.S. Pat. No. 5,026,687 to Yarchoan et al.),and benzimidazoles (U.S. Pat. No. 5,891,874 to Colacino et al.).

(16) Other compounds currently in clinical development for treatment ofhepatitis c virus include: Interleukin-10 by Schering-Plough, IP-501 byInterneuron, Merimebodib VX-497 by Vertex, AMANTADINE (Symmetrel) byEndo Labs Solvay, HEPTAZYME by RPI, IDN-6556 by Idun Pharma., XTL-002 byXTL., HCV/MF59 by Chiron, CIVACIR by NABI, LEVOVIRIN by ICN, VIRAMIDINEby ICN, ZADAXIN (thymosin alfa-1) by Sci Clone, CEPLENE (histaminedihydrochloride) by Maxim, V X 950/LY 570310 by Vertex/Eli Lilly, ISIS14803 by Isis Pharmaceutical/Elan, IDN-6556 by Idun Pharmaceuticals,Inc. and JTK 003 by AKROS Pharma.

Drug-resistant variants of viruses can emerge after prolonged treatmentwith an antiviral agent. Drug resistance most typically occurs bymutation of a gene that encodes for an enzyme used in viral replication,and, for example, in the case of HIV, reverse transcriptase, protease,or DNA polymerase. It has been demonstrated that the efficacy of a drugagainst viral infection can be prolonged, augmented, or restored byadministering the compound in combination or alternation with a second,and perhaps third, antiviral compound that is effective in combating thevirus. The pharmacokinetics, biodistribution, or other parameter of thedrug can be altered by such combination or alternation therapy. Ingeneral, combination therapy is typically preferred over alternationtherapy because it induces multiple simultaneous pressures on the virus.One cannot predict, however, what mutations will be induced in the viralgenome by a given drug, whether the mutation is permanent or transient,or how an infected cell with or without a mutated viral sequence willrespond to therapy with other agents in combination or alternation. Thisis exacerbated by the fact that there is a paucity of data on thekinetics of drug resistance in long-term cell cultures treated withmodern antiviral agents.

It is an object of the present invention to optimize the treatment ofHCV infection.

It is a further object to provide the optimal administration of2′-branched nucleosides, and in particular, 2′-branched pyrimidinenucleosides, for the treatment of Flaviviridae infections.

It is another object of the present invention to provide a method andcomposition that includes 2′-branched nucleosides for the treatment ofpatients infected with pestiviruses, Flaviviruses, or hepaciviruses thatexhibit advantageous or improved pharmacokinetic, biodistribution,metabolic, resistance or other parameters over administration of2′-branched pyrimidine nucleosides alone.

It is yet another object of the present invention to provide a methodand composition for the treatment of patients infected with Flaviviridaein which 2′-branched nucleosides, and in particular, 2′-branchedpyrimidine nucleosides are administered in combination and/oralternation with one or more compounds that act synergistically oradvantageously with 2′-branched pyrimidine nucleosides against thevirus.

It is still another object of the present invention to provide a methodand composition for the treatment of patients infected with a drugresistant form of pestiviruses, Flaviviruses, or hepaciviruses.

It is also an object of the invention to provide a method and kit toidentify a mutant strain of Flaviviridae.

SUMMARY OF THE INVENTION

It has been discovered that prolonged use of a 2′-branched nucleoside,for example a 2′-branched nucleoside depicted below, and in particular,a 2′-branched pyrimidine nucleoside, such as the compoundβ-D-2′-CH₃-riboC, or a 2′-branched purine nucleoside, including thecompound β-D-2′-CH₃-riboAdenosine or β-D-2′-CH3-ribo-6-N-methyl aminoadenosine, is associated with a mutation at a nucleotide that encodesfor serine in the highly conserved consensus sequence, XRXSGXXXT (SEQ IDNO: 63), of domain B of the RNA polymerase region (FIG. 11) ofFlaviviridae, which results in a change in the amino acid residue serineto a different amino acid, for example, threonine. This domain is foundin the NS5B region of the HCV genome, as well as in genomes of otherflaviviruses. It is highly conserved among all hepaci-, pesti- andflavivirus genomes (FIG. 11, Lai et al. J. Virol. 1999, 73, 10129-36).

In one embodiment of the invention, the 2′-branched nucleoside is of thegeneral formula:

or its pharmaceutically acceptable prodrug and/or salt, wherein

-   R¹, R², and R³ are independently H, phosphate (including mono-, di-    or triphosphate and a stabilized phosphate prodrug); acyl (including    lower acyl); alkyl (including lower alkyl); sulfonate ester    (including alkyl or arylalkyl sulfonyl including methanesulfonyl);    benzyl, wherein the phenyl group is optionally substituted with one    or more substituents as described in the definition of aryl given    herein; lipid (including a phospholipid); amino acid; carbohydrate;    peptide; cholesterol; or a pharmaceutically acceptable leaving group    that provides a compound wherein R¹, R² or R³ is independently H or    phosphate when administered in vivo; and-   R⁴ is hydrogen, hydroxy, alkyl (including lower alkyl), azido,    cyano, alkenyl, alkynyl, Br-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), chloro, bromo, fluoro, iodo, NO₂, NH₂, —NH(lower    alkyl), —NH(acyl), —N(lower alkyl)₂, or —N(acyl)₂;    and Base is a purine or pyrimidine as further described herein.

In a second embodiment of the invention, the 2′-branched nucleoside isof the general formula:

or its pharmaceutically acceptable prodrug and/or salt, whereinBase is a purine or pyrimidine base as defined herein;

-   R¹, R² and R³ are independently H, phosphate (including mono-, di-    or triphosphate and a stabilized phosphate); straight chained,    branched or cyclic alkyl (including lower alkyl); acyl (including    lower acyl); CO-alkyl, CO-aryl, CO-alkoxyalkyl, CO-aryloxyalkyl,    CO-substituted aryl, sulfonate ester (including alkyl or arylalkyl    sulfonyl including methanesulfonyl); benzyl, wherein the phenyl    group is optionally substituted with one or more substituents as    described in the definition of aryl given herein; alkylsulfonyl,    arylsulfonyl, aralkylsulfonyl, lipid (including a phospholipid);    amino acid; carbohydrate; peptide; cholesterol; or a    pharmaceutically acceptable leaving group that provides a compound    wherein R¹, R² or R³ is independently H or phosphate when    administered in vivo;-   R⁶ is alkyl (including lower alkyl and halogenated alkyl), CH₃, CF₃,    azido, cyano, alkenyl, alkynyl, Br-vinyl, 2-Br-ethyl, —C(O)O(alkyl),    —C(O)O(lower alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower    alkyl), —O(alkenyl), CF₃, chloro, bromo, fluoro, iodo, NO₂, NH₂,    —NH(lower alkyl), —NH(acyl), —N(lower alkyl)₂, —N(acyl)₂; and-   R⁷ is hydrogen, OR³, hydroxy, alkyl (including lower alkyl), azido,    cyano, alkenyl, alkynyl, Br-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), fluorine, chlorine, bromine, iodine, NO₂, NH₂,    —NH(lower alkyl), —NH(acyl), —N(lower alkyl)₂, —N(acyl)₂; and-   X is O, S, SO₂ or CH₂.    and Base is a purine or pyrimidine as further described herein.

In a third embodiment the invention, the 2′-branched nucleoside is ofthe general formula:

wherein:Base is a purine or pyrimidine base as defined herein;

-   R⁶ is alkyl (including lower alkyl and halogenated alkyl), CH₃, CF₃,    azido, cyano, alkenyl, alkynyl, Br-vinyl, 2-Br-ethyl, —C(O)O(alkyl),    —C(O)O(lower alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower    alkyl), —O(alkenyl), CF₃, fluoro, chloro, bromo, iodo, NO₂, NH₂,    —NH(lower alkyl), —NH(acyl), —N(lower alkyl)₂, —N(acyl)₂;-   R⁷ is OR², hydroxy, alkyl (including lower alkyl), azido, cyano,    alkenyl, alkynyl, Br-vinyl, halo-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), fluorine, chlorine, bromine, iodine, NO₂, NH₂,    —NH(lower alkyl), —NH(acyl), —N(lower alkyl)₂, —N(acyl)₂;-   R⁹ is hydrogen, OR³, hydroxy, alkyl (including lower alkyl), azido,    cyano, alkenyl, alkynyl, Br-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), chlorine, bromine, iodine, NO₂, NH₂, —NH(lower alkyl),    —NH(acyl), —N(lower alkyl)₂, —N(acyl)₂;-   R¹⁰ is H, alkyl (including lower alkyl), fluorine, chlorine, bromine    or iodine;-   R¹, R² and R³ are independently H, phosphate (including mono-, di-    or triphosphate and a stabilized phosphate); straight chained,    branched or cyclic alkyl (including lower alkyl); acyl (including    lower acyl); CO-alkyl, CO-aryl, CO-alkoxyalkyl, CO-aryloxyalkyl,    CO-substituted aryl, sulfonate ester (including alkyl or arylalkyl    sulfonyl including methanesulfonyl); benzyl, wherein the phenyl    group is optionally substituted with one or more substituents as    described in the definition of aryl given herein; alkylsulfonyl,    arylsulfonyl, aralkylsulfonyl, lipid (including a phospholipid);    amino acid; carbohydrate; peptide; cholesterol; or a    pharmaceutically acceptable leaving group that provides a compound    wherein R¹, R² or R³ is independently H or phosphate when    administered in vivo; and-   X is O, S, SO₂ or CH₂.

In the case of BVDV infection, 2′-branched nucleosides, and, inparticular, 2′-branched pyrimidine nucleosides such as the compoundβ-D-2′-CH₃-riboC induce a mutation from a guanine (G) to cytidine (C) atreside 1214 of the RNA polymerase of BVDV, which results in a change inthe amino acid residue serine to threonine at position 405 of theenzyme. This serine residue is located in the conserved consensussequence (XRXSGXXXT (SEQ ID NO: 63)) of the RNA polymerase domain B(FIGS. 5 and 11), identified by mutational analysis (Lai V. C., Kao C.C., Ferrari E., Park J., Uss A. S., Wright-Minogue J., Hong Z., and J.Y. Lau. “Mutational analysis of bovine viral diarrhea virusRNA-dependent RNA polymerase” J. Virol. 1999, 73, 10129-36).

In the case of HCV infection, 2′-branched nucleosides, and, inparticular, 2′-branched pyrimidine nucleosides such as the compoundβ-D-2′-CH₃-riboC induce a mutation at a nucleotide that encodes forSerine₂₈₂ in the highly conserved consensus sequence, XRXSGXXXT (SEQ IDNO: 63), of domain B of the RNA polymerase region (FIG. 11), whichresults in a change from serine to a different amino acid, such asthreonine.

Furthermore, it has been discovered that 2′-branched nucleosides andinterferon act synergistically to inhibit Flaviviridae. In particular2′-branched pyrimidine nucleosides such as the compound β-D-2′-CH₃-riboCor a 2′-branched purine nucleosides such as the compoundβ-D-2′-CH3-riboA or β-D-2′-CH3-ribo-6-N-methyl amino adenosine, andinterferon alpha-2b administered in combination and/or alternation actsynergistically to inhibit Flaviviridae. Moreover, it has beendiscovered that the resistant viral populations, which emerge after2′-branched nucleoside treatment, for example, β-D-2′-CH₃-riboCtreatment, show increased sensitivity to subsequent treatment withinterferon. Thus, sequential and/or combination therapy of a 2′-branchednucleoside and interferon can substantially reduce Flaviviridaeinfections.

One aspect of the present invention provides a method to treat aFlaviviridae infection by administering a therapeutically effectiveamount of a 2′-branched nucleoside, for example, a 2′-branchedpyrimidine nucleoside, for example β-D-2′-CH₃-riboC, or itspharmaceutically acceptable prodrug and/or salt, to a host, such as ahuman, in need of such therapy, in combination and/or alternation withone or more drugs that directly or indirectly induce a mutation in aFlaviviridae at a location other than a mutation of a nucleotide thatresults in a change from serine to a different amino acid in the highlyconserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B ofthe RNA polymerase region, and/or one or more drugs that are associatedwith such a mutation. This highly conserved serine residue correspondsto amino acid position 405 of the RNA polymerase region of the BVDVgenome. It also corresponds to amino acid position 282 of the RNApolymerase region of the HCV genome (FIG. 11; Lai et al. J Virol., 1999,73, 10129-36).

Another aspect of the present invention provides a method to treatand/or to substantially cure a Flaviviridae infection in a host infectedwith a Flaviviridae that contains a serine to threonine mutation at theconserved serine residue of a Flaviviridae (FIG. 11), for example, aminoacid 405 of the RNA polymerase region of BVDV or amino acid 282 of theRNA polymerase of HCV, by administering a therapeutically effectiveamount of interferon. In a specific embodiment, interferon alpha-2b isadministered to treat and/or to substantially cure the infection causedby a mutated Flaviviridae virus.

The invention disclosed herein also minimally includes at least thefollowing embodiments:

-   (i) A pharmaceutical composition effective for the treatment of a    Flaviviridae infection in a host, such as a human, comprising an    effective amount of a 2′-branched nucleoside, for example, a    2′-branched nucleoside, such as β-D-2′-branched pyrimidine    nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as the    3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched    purine nucleoside, for example β-D-2′-CH₃-riboA or    β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the    3′-valine ester prodrug, or its pharmaceutically acceptable prodrug    and/or salt, optionally in a pharmaceutically acceptable carrier or    diluent, in combination with one or more drugs that directly or    indirectly induce a mutation in a Flaviviridae at a location other    than a mutation of a nucleotide that results in a change from serine    to a different amino acid in the highly conserved consensus    sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B of the RNA    polymerase region, for example, other than nucleotide 1214 (G to C)    or 405 Ser to Thr of the RNA polymerase region of BVDV or nucleotide    8443 (G to C) of the HCV genome or 282 Ser to Thr of the RNA    polymerase region of HCV (FIG. 11; Lai et al. J. Virol., 1999, 73,    10129-36), and/or one or more drugs that are associated with such a    mutation.-   (ii) A pharmaceutical composition effective for the treatment of a    Flaviviridae infection in a host, such as a human, comprising an    effective amount of a 2′-branched nucleoside, such as    β-D-2′-branched pyrimidine nucleoside, for example β-D-2′-CH₃-riboC    or a prodrug, such as the 3′-valine ester prodrug of    β-D-2′-CH₃-riboC, or a β-D-2′-branched purine nucleoside, for    example β-D-2′-CH₃-riboA or β-D-2′-CH₃-ribo-6-N-methylaminopurine or    a prodrug, such as the 3% valine ester prodrug, or a    pharmaceutically acceptable prodrug and/or salt thereof, optionally    in a pharmaceutically acceptable carrier or diluent, in combination    with interferon. Interferons include: Intron-A (interferon alpha-2b)    by Schering, PEG-INTRON (pegylated interferon alpha-2b) by Schering,    Roferon-A (interferon alfa-2a) by Roche, PEGASYS (pegylated    interferon alfa-2a) by Roche, INFERGEN (interferon alfacon-1) by    InterMune, OMNIFERON (natural interferon) by Viragen, ALBUFERON by    Human Genome Sciences, REBIF (interferon beta-1a) by Ares-Serono,    Omega Interferon by BioMedicine, Oral Interferon Alpha by Amarillo    Biosciences, and Interferon gamma-1b by InterMune.-   (iii) A pharmaceutical composition effective for the treatment of a    Flaviviridae infection in a host, such as a human, comprising:    -   an effective amount of a 2′, 3′ and/or 5′-prodrug of a        2′-branched nucleoside, such as β-D-2′-branched pyrimidine        nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, including        the 3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a        β-D-2′-branched purine nucleoside, for example β-D-2′-CH₃-riboA        or β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, including        the 3′-valine ester prodrug, or a pharmaceutically acceptable        salt thereof, or a pharmaceutically acceptable salt thereof,        optionally in a pharmaceutically acceptable carrier or diluent;    -   in combination with one or more drugs that directly or        indirectly induce a mutation in a Flaviviridae at a location        other than a mutation of a nucleotide that results in a change        from serine to a different amino acid in the highly conserved        consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B of        the RNA polymerase region, and/or one or more drugs that are        associated with such a mutation.-   (iv) A method for treating a Flaviviridae infection in a host, such    as a human, comprising administering an effective amount of a    2′-branched nucleoside, such as β-D-2′-branched pyrimidine    nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as the    3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched    purine nucleoside, for example β-D-2′-CH₃-riboA or    β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the    3′-valine ester prodrug, or its pharmaceutically acceptable prodrug    and/or salt to the human, optionally in a pharmaceutically    acceptable carrier or diluent, in combination and/or alternation    with one or more drugs that directly or indirectly induce a mutation    in a Flaviviridae at a location other than a mutation of a    nucleotide that results in a change from serine to a different amino    acid in the highly conserved consensus sequence, XRXSGXXXT (SEQ ID    NO: 63), of domain B of the RNA polymerase region, for example,    other than nucleotide 1214 (G to C) or 405 Ser to Thr of the RNA    polymerase region of BVDV or nucleotide 8443 (G to C) of the HCV    genome or 282 Ser to Thr of the RNA polymerase region of HCV (FIG.    11; Lai et al. J. Virol., 1999, 73, 10129-36), and/or one or more    drugs that are associated with such a mutation.-   (v) A method for treating a Flaviviridae infection in a host, such    as a human, comprising administering an effective amount of a    2′-branched nucleoside, such as β-D-2′-branched pyrimidine    nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as the    3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched    purine nucleoside, for example β-D-2′-CH₃-riboA or    β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the    3′-valine ester prodrug, or a pharmaceutically acceptable prodrug    and/or salt thereof to the host, optionally in a pharmaceutically    acceptable carrier or diluent, in combination and/or alternation    with interferon. Interferons include: Intron-A (interferon alpha-2b)    by Schering, PEG-INTRON (pegylated interferon alpha-2b) by Schering,    Roferon-A (interferon alfa-2a) by Roche, PEGASYS (pegylated    interferon alfa-2a) by Roche, INFERGEN (interferon alfacon-1) by    InterMune, OMNIFERON (natural interferon) by Viragen, ALBUFERON by    Human Genome Sciences, REBIF (interferon beta-1a) by Ares-Serono,    Omega Interferon by BioMedicine, Oral Interferon Alpha by Amarillo    Biosciences, and Interferon gamma-1b by InterMune.-   (vi) A method for treating a patient infected with a Flaviviridae    virus that is resistant to a 2′-branched nucleoside, such as    β-D-2′-branched pyrimidine nucleoside, for example β-D-2′-CH₃-riboC    or a prodrug, such as the 3′-valine ester prodrug of    β-D-2′-CH₃-riboC, or a β-D-2′-branched purine nucleoside, for    example β-D-2′-CH₃-riboA or β-D-2′-CH₃-ribo-6-N-methylaminopurine or    a prodrug, such as the 3′-valine ester prodrug, or a    pharmaceutically acceptable salt thereof, comprising administering    an effective amount of interferon, optionally in a pharmaceutically    acceptable carrier or diluent, optionally in a manner that    substantially eliminates the viral load.-   (iv) A method for treating a patient infected with Flaviviridae    comprising:    -   administering an effective amount of a 2′, 3′ and/or 5′-prodrug        of a 2′-branched nucleoside, such as β-D-2′-branched pyrimidine        nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as        the 3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a        β-D-2′-branched purine nucleoside, for example β-D-2′-CH₃-riboA        or β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as        the 3′-valine ester prodrug, or a pharmaceutically acceptable        salt thereof, optionally in a pharmaceutically acceptable        carrier or diluent;    -   in combination and/or alternation with one or more drugs that        directly or indirectly induce a mutation in a Flaviviridae at a        location other than a mutation of a nucleotide that results in a        change from serine to a different amino acid in the highly        conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of        domain B of the RNA polymerase region, and/or one or more drugs        that are associated with such a mutation.-   (v) A method for treating a patient infected with Flaviviridae    comprising:    -   (a) administering to the patient an effective amount of a        2′-branched nucleoside, such as β-D-2′-branched pyrimidine        nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as        the 3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a        β-D-2′-branched purine nucleoside, for example β-D-2′-CH₃-riboA        or β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as        the 3′-valine ester prodrug, or a pharmaceutically acceptable        salt thereof; optionally in a pharmaceutically acceptable        carrier or diluent;    -   (b) assaying the blood of the patient to test for seroconversion        from wildtype to mutant virus; and    -   (c) administering an effective amount of interferon; optionally        in a pharmaceutically acceptable carrier or diluent.-   (vi) A method for assaying a sample suspected of containing a    Flaviviridae resistant to a 2′-branched nucleoside, such as    β-D-2′-branched pyrimidine nucleoside, for example β-D-2′-CH₃-riboC    or a prodrug, such as the 3′-valine ester prodrug of    β-D-2′-CH₃-riboC, or a β-D-2′-branched purine nucleoside, for    example β-D-2′-CH₃-riboA or β-D-2′-CH₃-ribo-6-N-methylaminopurine or    a prodrug, such as the 3′-valine ester prodrug, or a    pharmaceutically acceptable salt thereof; comprising:    -   (a) contacting a sample containing a Flaviviridae nucleic acid        sequence with a detectable oligonucleotide probe having a        sequence complementary a codon that encodes a serine in the        highly conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63),        of domain B of the RNA polymerase region of Flaviviridae (FIG.        11);    -   (b) allowing the probe to hybridize to the sequence; and    -   (c) detecting the hybridization of the probe the sequence.-   (vii) A method for assaying a sample suspected of containing a    Flaviviridae resistant to a 2′-branched nucleoside, such as    β-D-2′-branched pyrimidine nucleoside, for example β-D-2′-CH₃-riboC    or a prodrug, such as the 3′-valine ester prodrug of    β-D-2′-CH₃-riboC, or a β-D-2′-branched purine nucleoside, for    example β-D-2′-CH₃-riboA or β-D-2′-CH₃-ribo-6-N-methylaminopurine or    a prodrug, such as the 3′-valine ester prodrug, or a    pharmaceutically acceptable salt thereof; comprising:    -   (a) contacting a sample containing a Flaviviridae nucleic acid        sequence with a detectable oligonucleotide probe having a        sequence complementary to the cytidine at nucleotide 1214 of the        RNA polymerase region of BVDV or the cytidine at nucleotide 8443        of HCV;    -   (b) allowing the probe to hybridize to the sequence; and    -   (c) detecting the hybridization of the probe to cytidine at        nucleotide 1214 of the RNA polymerase region of BVDV or at        nucleotide 8443 of HCV.-   (viii) A method for treating a patient infected with Flaviviridae    comprising:    -   (a) administering an effective amount of a 2′-branched        nucleoside, such as β-D-2′-branched pyrimidine nucleoside, for        example β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine        ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof; optionally in a pharmaceutically acceptable carrier or        diluent;    -   (b) obtaining a viral sample from the patient;    -   (c) determining the replication fitness of the virus;    -   (d) determining whether the replication fitness of the virus in        the sample is less than the replication fitness of the wild-type        virus, which indicates resistance to the 2′-branched nucleoside,        such as β-D-2′-branched pyrimidine nucleoside, for example        β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine ester        prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof; and    -   (e) administering an effective amount of interferon to those        patients that are resistant to the 2′-branched nucleoside, such        as β-D-2′-branched pyrimidine nucleoside, for example        β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine ester        prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof.-   (ix) A method for treating a patient infected with Flaviviridae    comprising:    -   (a) administering an effective amount of a 2′-branched        nucleoside, such as β-D-2′-branched pyrimidine nucleoside, for        example β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine        ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof; optionally in a pharmaceutically acceptable carrier or        diluent;    -   (b) obtaining a viral culture sample from the patient;    -   (c) culturing the sample and comparing the plaque growth between        the sample and wild type virus;    -   (d) determining whether the plaque growth of the sample is        smaller than the plaque growth of the wildtype, which indicates        resistance to the 2′-branched nucleoside; and    -   (e) administering an effective amount of interferon to those        patients that are resistant to the 2′-branched nucleoside, such        as β-D-2′-branched pyrimidine nucleoside, for example        β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine ester        prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof.-   (x) A method for diagnosing the presence of a Flaviviridae resistant    to a 2′-branched nucleoside, such as β-D-2′-branched pyrimidine    nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as the    3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched    purine nucleoside, for example β-D-2′-CH₃-riboA or    β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the    3′-valine ester prodrug, or a pharmaceutically acceptable salt    thereof, in a patient comprising:    -   (a) obtaining a sample suspected of containing a Flaviviridae        nucleic acid sequence;    -   (b) contacting the sample with a detectable oligonucleotide        probe having a sequence complementary a codon that encodes a        serine in the highly conserved consensus sequence, XRXSGXXXT        (SEQ ID NO: 63), of domain B of the RNA polymerase region of        Flaviviridae (FIG. 11);    -   (b) allowing the probe to hybridize to the sequence; and    -   (c) detecting the hybridization of the probe the sequence to        determine the presence of a Flaviviridae resistant to the        2′-branched nucleoside, such as β-D-2′-branched pyrimidine        nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as        the 3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a        β-D-2′-branched purine nucleoside, for example β-D-2′-CH₃-riboA        or β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as        the 3′-valine ester prodrug, or a pharmaceutically acceptable        salt thereof.-   (xi) A method for diagnosing of the presence of a Flaviviridae    resistant to the 2′-branched nucleoside, such as β-D-2′-branched    pyrimidine nucleoside, for example β-D-2′-CH₃-riboC or a prodrug,    such as the 3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a    β-D-2′-branched purine nucleoside, for example β-D-2′-CH₃-riboA or    β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the    3′-valine ester prodrug, or a pharmaceutically acceptable salt    thereof, in a patient comprising:    -   (a) obtaining a sample suspected of containing a Flaviviridae        nucleic acid sequence;    -   (b) contacting the sample with a detectable oligonucleotide        probe having a sequence complementary to the cytidine at        nucleotide 1214 of the RNA polymerase region of BVDV or the        cytidine at nucleotide 8443 of HCV;    -   (b) allowing the probe to hybridize to the sequence; and    -   (c) detecting the hybridization of the probe to cytidine at        nucleotide 1214 of the RNA polymerase region of BVDV or at        nucleotide 8443 of HCV to determine the presence of a        Flaviviridae resistant to to the 2′-branched nucleoside, such as        β-D-2′-branched pyrimidine nucleoside, for example        β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine ester        prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof.

The disclosed combination and/or alternation regimens are useful in theprevention and treatment of Flaviviridae infections, including BVDV,BDV, CSFV, DHF, yellow fever virus, shock syndrome, Japaneseencephalitis virus, and HCV.

In addition, the corresponding amino acid sequences of the Flaviviridaeviral markers diagnostic for long term response of Flaviviridae carriersto 2′-branched nucleoside therapy can be determined from theillustrative Flaviviridae nucleotide sequences.

In addition to identifying viral markers for the purposes of identifyingFlaviviridae strains that are associated with 2′-branched nucleosidefailure, the present invention can be utilized to also identifyFlaviviridae strains that respond to 2′-branched nucleoside therapy. Inthis respect, the absence of viral markers correlated with 2′-branchednucleoside therapy can be used to prescribe a course of treatment thatincludes 2′-branched nucleoside as a modality for those individuals thatcarrier Flaviviridae lacking viral markers correlated with 2′-branchednucleoside therapy failure.

In another embodiment, the invention provides an oligonucleotide primerfor amplifying an Flaviviridae nucleic acid sequence. In one embodiment,the oligonucleotide is at least 14 nucleotides in length and hybridizesunder sequence-specific, stringent hybridization conditions to anucleotide sequence that contains the marker correlated with therapyfailure.

Oligonucleotide sequences used as the hybridizing region of a primer canalso be used as the hybridizing region of a probe. Suitability of aprimer sequence for use as a probe depends on the hybridizationcharacteristics of the primer. Similarly, an oligonucleotide used as aprobe can be used as a primer.

Additionally, the invention provides a method, materials and a kit todetect proteins, peptides or peptide fragments that contain amino acids(as described extensively herein) that are predictive of the long termresponse of an Flaviviridae carrier to 2′-branched nucleoside therapy,or antibodies to those proteins, peptides or peptide fragments. Hostsera or tissue can be tested for either the protein or peptide or theantibody to the protein or peptide, depending on convenience and perhapsconcentration of the diagnostic material.

The protein, peptide or peptide fragment can be confirmed by reactionwith an antibody, preferably a monoclonal antibody, for example using aWestern blot method. Alternatively, the protein or peptide can beisolated and sequenced or otherwise identified by any means known in theart, including by 2D PAGE. In one embodiment, a reactive antibody bindsto an Flaviviridae protein or peptide sequence that includes a threoninerather than serine in the highly conserved consensus sequence, XRXSGXXXT(SEQ ID NO: 63), of domain B of the RNA polymerase region, for exampleat position 405 of the RNA polymerase region of BVDV genome or atposition 282 of the RNA polymerase region of the HCV genome.

In another embodiment, the reactive antibody binds specifically to apeptide sequence that includes a threonine rather than serine in thehighly conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), ofdomain B of the RNA polymerase region, for example at position 405 ofthe RNA polymerase region of BVDV genome or at position 282 of the RNApolymerase region of the HCV genome, which represent a specific pointmutations in the RNA polymerase region of Flaviviridae that iscorrelated with therapy failure.

In specific embodiments, an antibody is used that binds to at least onepeptide or peptide fragment encoded for by the nucleic acid sequences insequence ID Nos. 1-31.

In specific embodiments, an antibody is used that binds to at least onepeptide or peptide fragment encoded for by the nucleic acid sequences insequence ID Nos.32-62.

BRIEF DESCRIPTION OF THE FIGURES

FIG. 1 shows the emergence of β-D-2′-CH₃-riboC-resistant BVDV fromuntreated BVDV.

FIG. 2 illustrates the phenotype of focus formation by (A) the wild type(wt) BVDV (strain I-N-dIns), and by (B) the β-D-2′-CH₃-riboC-resistantBVDV (I-N-dIns β-D-2′-CH₃-riboC-R).

FIG. 3 demonstrates the growth kinetics of wild-type BVDV I-N-dIns andits β-D-2′-CH₃-riboC-resistant mutant, I-N-dIns β-D-2′-CH₃-riboC-R(Resistant Mutant).

FIG. 4 shows the effect of β-D-2′-CH₃-riboC on the virus yield in denovo-infected MDBK cells (wherein I-N-dIns is wt BVDV, and the resistantmutatnt is I-N-dIns β-D-2′-CH₃-riboC-R (β-D-2′-CH₃-riboC-resistantBVDV)).

FIG. 5 is a schematic representation of the BVDV NS5B region showing theproposed functional domains, based on the mutational analysis (Vassilev,V. B. and R. O. Donis. (2000) Bovine viral diarrhea virus inducedapoptosis correlates with increased intracellular viral RNAaccumulation. Virus Res. 69 (2): 95-107). The large arrow indicates theposition of the only amino acid change found in the NS5B region of theβ-D-2′-CH₃-riboC—resistant BVDV (Ser 405 to Thr 405).

FIG. 6 illustrates the effect of interferon alpha-2b on the virus yieldsin de novo-infected MDBK cells (I-N-dIns: wt BVDV; I-N-dInsβ-D-2′-CH₃-riboC-R: β-D-2′-CH₃-riboC-resistant BVDV (resistant mutant)).

FIG. 7 illustrates the effect of β-D-2′-CH₃-riboC and interferonalpha-2b on BVDV (strain I-N-dIns) titers in persistently infected MDBKcells

FIG. 8 demonstrates the effect of β-D-2′-CH₃-riboC in combination withinterferon alpha-2b on wild-type BVDV (strain I-N-dIns) titers inpersistently infected MDBK cells.

FIG. 9 shows the effect of β-D-2′-CH₃-riboC and interferon alpha-2b(Intron A) on BVDV (strain NY-1) titers in persistently infected MDBKcells.

FIG. 10 illustrates the effect of β-D-2′-CH₃-riboC and interferonalpha-2b (Intron A) on wild-type BVDV (strain I-N-dIns) titers inpersistently infected MDBK cells.

FIG. 11 illustrates the alignment of the RNA Polymerase in domain B ofvarious Flaviviridae; bold type with larger font show amino acids thatare 100% conserved; underlined serine amino acid residues are ones thatmay be mutated to threonine after treatment with a 2′-branchednucleoside. [The 100% conserved serine residue is also underlined andrepresents the amino acid that is mutated to Threonine after treatmentwith a 2′-branched nucleoside (Ser₄₀₅ of the RNA polymerase region ofBVDV; Ser₂₈₂ of the RNA polymerase region of HCV). See Lai et al. JVirol. 1999, 73, 10129-36.]

DETAILED DESCRIPTION OF THE INVENTION

It has been discovered that prolonged use of a 2′-branched nucleoside,for example a 2′-branched nucleoside depicted below, and in particular,a 2′-branched pyrimidine nucleoside such as the compoundβ-D-2′-CH₃-riboC, is associated with a mutation at a nucleotide thatencodes for serine in the highly conserved consensus sequence, XRXSGXXXT(SEQ ID NO: 63), of domain B of the RNA polymerase region (FIG. 11) ofFlaviviridae resulting in a change in the amino acid residue serine to adifferent amino acid, for example, threonine. This domain is found inthe NS5B region of the HCV genome, as well as in genomes of otherflaviviruses. It is highly conserved among all hepaci-, pesti- andflavivirus genomes (FIG. 11, Lai et al. J. Virol. 1999, 73, 10129-36).

In the case of BVDV infection, 2′-branched nucleosides, and, inparticular, 2′-branched pyrimidine nucleosides such as the compoundβ-D-2′-CH₃-riboC induce a mutation from a guanine (G) to cytidine (C) atreside 1214 of the RNA polymerase of BVDV causing a change in the aminoacid residue serine to threonine at position 405 of the enzyme. Thisserine residue is located in the conserved consensus sequence (XRXSGXXXT(SEQ ID NO: 63)) of the RNA polymerase domain B (FIGS. 5 and 11),identified by mutational analysis (Lai V. C., Kao C. C., Ferrari E.,Park J., Uss A. S., Wright-Minogue J., Hong Z., and J. Y. Lau.“Mutational analysis of bovine viral diarrhea virus RNA-dependent RNApolymerase” J. Virol. 1999, 73, 10129-36).

In the case of HCV infection, 2′-branched nucleosides, and, inparticular, 2′-branched pyrimidine nucleosides such as the compoundβ-D-2′-CH₃-riboC induce a mutation at a nucleotide that encodes forSerine₂₈₂ in the highly conserved consensus sequence, XRXSGXXXT (SEQ IDNO: 63), of domain B of the RNA polymerase region (FIG. 11) resulting ina change from serine to a different amino acid, such as threonine.

Furthermore, it has been discovered that 2′-branched nucleosides andinterferon act synergistically to inhibit Flaviviridae. In particular2′-branched pyrimidine nucleosides such as the compound β-D-2′-CH₃-riboCand interferon alpha-2b administered in combination and/or alternationact synergistically to inhibit Flaviviridae. Moreover, it has beendiscovered that the resistant viral populations, which emerge after2′-branched nucleoside treatment, for example, β-D-2′-CH₃-riboCtreatment, show increased sensitivity to subsequent treatment withinterferon. Thus, sequential and/or combination therapy of a 2′-branchednucleoside and interferon can substantially reduce Flaviviridaeinfections.

One aspect of the present invention provides a method to treat aFlaviviridae infection by administering a therapeutically effectiveamount of a 2′-branched nucleoside, for example, a 2′-branchedpyrimidine nucleoside, for example β-D-2′-CH₃-riboC, or itspharmaceutically acceptable prodrug and/or salt, to a host, such as ahuman, in need of such therapy, in combination and/or alternation withone or more drugs that directly or indirectly induce a mutation in aFlaviviridae at a location other than a mutation of a nucleotide thatresults in a change from serine to a different amino acid in the highlyconserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B ofthe RNA polymerase region, and/or one or more drugs that are associatedwith such a mutation. This highly conserved serine residue correspondsto amino acid position 405 of the RNA polymerase region of the BVDVgenome. It also corresponds to amino acid position 282 of the RNApolymerase region of the HCV genome (FIG. 11; Lai et al. J. Virol.,1999, 73, 10129-36).

Another aspect of the present invention provides a method to treatand/or to substantially cure a Flaviviridae infection in a host infectedwith a Flaviviridae that contains a serine to threonine mutation at theconserved serine residue of a Flaviviridae (FIG. 11), for example, aminoacid 405 of the RNA polymerase region of BVDV or amino acid 282 of theRNA polymerase of HCV, by administering a therapeutically effectiveamount of interferon. In a specific embodiment, interferon alpha-2b isadministered to treat and/or to substantially cure the infection causedby a mutated Flaviviridae virus.

The invention disclosed herein also minimally includes at least thefollowing embodiments:

-   (i) A pharmaceutical composition effective for the treatment of a    Flaviviridae infection in a host, such as a human, comprising an    effective amount of a 2′-branched nucleoside, for example, a    2′-branched nucleoside, such as β-D-2′-branched pyrimidine    nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as the    3′-valine ester prodrug of β-D-2″-CH₃-riboC, or a β-D-2′-branched    purine nucleoside, for example β-D-2′-CH₃-riboA or    β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the    3′-valine ester prodrug, or its pharmaceutically acceptable prodrug    and/or salt, optionally in a pharmaceutically acceptable carrier or    diluent, in combination with one or more drugs that directly or    indirectly induce a mutation in a Flaviviridae at a location other    than a mutation of a nucleotide that results in a change from serine    to a different amino acid in the highly conserved consensus    sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B of the RNA    polymerase region, for example, other than nucleotide 1214 (G to C)    or 405 Ser to Thr of the RNA polymerase region of BVDV or nucleotide    8443 (G to C) of the HCV genome or 282 Ser to Thr of the RNA    polymerase region of HCV (FIG. 11; Lai et al. J. Virol., 1999, 73,    10129-36), and/or one or more drugs that are associated with such a    mutation.-   (ii) A pharmaceutical composition effective for the treatment of a    Flaviviridae infection in a host, such as a human, comprising an    effective amount of a 2′-branched nucleoside, such as    β-D-2′-branched pyrimidine nucleoside, for example β-D-2′-CH₃-riboC    or a prodrug, such as the 3′-valine ester prodrug of    β-D-2′-CH₃-riboC, or a β-D-2′-branched purine nucleoside, for    example β-D-2′-CH₃-riboA or β-D-2′-CH₃-ribo-6-N-methylaminopurine or    a prodrug, such as the 3′-valine ester prodrug, or a    pharmaceutically acceptable prodrug and/or salt thereof, optionally    in a pharmaceutically acceptable carrier or diluent, in combination    with interferon. Interferons include: Intron-A (interferon alpha-2b)    by Schering, PEG-INTRON (pegylated interferon alpha-2b) by Schering,    Roferon-A (interferon alfa-2a) by Roche, PEGASYS (pegylated    interferon alfa-2a) by Roche, INFERGEN (interferon alfacon-1) by    InterMune, OMNIFERON (natural interferon) by Viragen, ALBUFERON by    Human Genome Sciences, REBIF (interferon beta-1a) by Ares-Serono,    Omega Interferon by BioMedicine, Oral Interferon Alpha by Amarillo    Biosciences, and Interferon gamma-1b by InterMune.-   (iii) A pharmaceutical composition effective for the treatment of a    Flaviviridae infection in a host, such as a human, comprising:    -   an effective amount of a 2′, 3′ and/or 5′-prodrug of a        2′-branched nucleoside, such as β-D-2′-branched pyrimidine        nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, including        the 3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a        β-D-2′-branched purine nucleoside, for example β-D-2′-CH₃-riboA        or β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, including        the 3′-valine ester prodrug, or a pharmaceutically acceptable        salt thereof, or a pharmaceutically acceptable salt thereof,        optionally in a pharmaceutically acceptable carrier or diluent;    -   in combination with one or more drugs that directly or        indirectly induce a mutation in a Flaviviridae at a location        other than a mutation of a nucleotide that results in a change        from serine to a different amino acid in the highly conserved        consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B of        the RNA polymerase region, and/or one or more drugs that are        associated with such a mutation.-   (iv) A method for treating a Flaviviridae infection in a host, such    as a human, comprising administering an effective amount of a    2′-branched nucleoside, such as β-D-2′-branched pyrimidine    nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as the    3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched    purine nucleoside, for example β-D-2′-CH₃-riboA or    β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the    3′-valine ester prodrug, or its pharmaceutically acceptable prodrug    and/or salt to the human, optionally in a pharmaceutically    acceptable carrier or diluent, in combination and/or alternation    with one or more drugs that directly or indirectly induce a mutation    in a Flaviviridae at a location other than a mutation of a    nucleotide that results in a change from serine to a different amino    acid in the highly conserved consensus sequence, XRXSGXXXT (SEQ ID    NO: 63), of domain B of the RNA polymerase region, for example,    other than nucleotide 1214 (G to C) or 405 Ser to Thr of the RNA    polymerase region of BVDV or nucleotide 8443 (G to C) of the HCV    genome or 282 Ser to Thr of the RNA polymerase region of HCV (FIG.    11; Lai et al. J. Virol., 1999, 73, 10129-36), and/or one or more    drugs that are associated with such a mutation.-   (v) A method for treating a Flaviviridae infection in a host, such    as a human, comprising administering an effective amount of a    2′-branched nucleoside, such as β-D-2′-branched pyrimidine    nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as the    3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched    purine nucleoside, for example β-D-2′-CH₃-riboA or    β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the    3′-valine ester prodrug, or a pharmaceutically acceptable prodrug    and/or salt thereof to the host, optionally in a pharmaceutically    acceptable carrier or diluent, in combination and/or alternation    with interferon. Interferons include: Intron-A (interferon alpha-2b)    by Schering, PEG-INTRON (pegylated interferon alpha-2b) by Schering,    Roferon-A (interferon alfa-2a) by Roche, PEGASYS (pegylated    interferon alfa-2a) by Roche, INFERGEN (interferon alfacon-1) by    InterMune, OMNIFERON (natural interferon) by Viragen, ALBUFERON by    Human Genome Sciences, REBIF (interferon beta-1a) by Ares-Serono,    Omega Interferon by BioMedicine, Oral Interferon Alpha by Amarillo    Biosciences, and Interferon gamma-1b by InterMune.-   (vi) A method for treating a patient infected with a Flaviviridae    virus that is resistant to a 2′-branched nucleoside, such as    β-D-2′-branched pyrimidine nucleoside, for example β-D-2′-CH₃-riboC    or a prodrug, such as the 3′-valine ester prodrug of    β-D-2′-CH₃-riboC, or a β-D-2′-branched purine nucleoside, for    example β-D-2′-CH₃-riboA or β-D-2′-CH₃-ribo-6-N-methylaminopurine or    a prodrug, such as the 3′-valine ester prodrug, or a    pharmaceutically acceptable salt thereof, comprising administering    an effective amount of interferon, optionally in a pharmaceutically    acceptable carrier or diluent, optionally in a manner that    substantially eliminates the viral load.-   (iv) A method for treating a patient infected with Flaviviridae    comprising:    -   administering an effective amount of a 2′, 3′ and/or 5′-prodrug        of a 2′-branched nucleoside, such as β-D-2′-branched pyrimidine        nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as        the 3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a        β-D-2′-branched purine nucleoside, for example β-D-2′-CH₃-riboA        or β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as        the 3′-valine ester prodrug, or a pharmaceutically acceptable        salt thereof, optionally in a pharmaceutically acceptable        carrier or diluent;    -   in combination and/or alternation with one or more drugs that        directly or indirectly induce a mutation in a Flaviviridae at a        location other than a mutation of a nucleotide that results in a        change from serine to a different amino acid in the highly        conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of        domain B of the RNA polymerase region, and/or one or more drugs        that are associated with such a mutation.-   (v) A method for treating a patient infected with Flaviviridae    comprising:    -   (a) administering to the patient an effective amount of a        2′-branched nucleoside, such as β-D-2′-branched pyrimidine        nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as        the 3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a        β-D-2′-branched purine nucleoside, for example β-D-2′-CH₃-riboA        or β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as        the 3′-valine ester prodrug, or a pharmaceutically acceptable        salt thereof; optionally in a pharmaceutically acceptable        carrier or diluent;    -   (b) assaying the blood of the patient to test for seroconversion        from wildtype to mutant virus; and    -   (c) administering an effective amount of interferon; optionally        in a pharmaceutically acceptable carrier or diluent.-   (vi) A method for assaying a sample suspected of containing a    Flaviviridae resistant to a 2′-branched nucleoside, such as    β-D-2′-branched pyrimidine nucleoside, for example β-D-2′-CH₃-riboC    or a prodrug, such as the 3′-valine ester prodrug of    β-D-2′-CH₃-riboC, or a β-D-2′-branched purine nucleoside, for    example β-D-2′-CH₃-riboA or β-D-2′-CH₃-ribo-6-N-methylaminopurine or    a prodrug, such as the 3′-valine ester prodrug, or a    pharmaceutically acceptable salt thereof; comprising:    -   (a) contacting a sample containing a Flaviviridae nucleic acid        sequence with a detectable oligonucleotide probe having a        sequence complementary a codon that encodes a serine in the        highly conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63),        of domain B of the RNA polymerase region of Flaviviridae (FIG.        11);    -   (b) allowing the probe to hybridize to the sequence; and    -   (c) detecting the hybridization of the probe the sequence.-   (vii) A method for assaying a sample suspected of containing a    Flaviviridae resistant to a 2′-branched nucleoside, such as    β-D-2′-branched pyrimidine nucleoside, for example β-D-2′-CH₃-riboC    or a prodrug, such as the 3′-valine ester prodrug of    β-D-2′-CH₃-riboC, or a β-D-2′-branched purine nucleoside, for    example β-D-2′-CH₃-riboA or β-D-2′-CH₃-ribo-6-N-methylaminopurine or    a prodrug, such as the 3′-valine ester prodrug, or a    pharmaceutically acceptable salt thereof; comprising:    -   (a) contacting a sample containing a Flaviviridae nucleic acid        sequence with a detectable oligonucleotide probe having a        sequence complementary to the cytidine at nucleotide 1214 of the        RNA polymerase region of BVDV or the cytidine at nucleotide 8443        of HCV;    -   (b) allowing the probe to hybridize to the sequence; and    -   (c) detecting the hybridization of the probe to cytidine at        nucleotide 1214 of the RNA polymerase region of BVDV or at        nucleotide 8443 of HCV.-   (viii) A method for treating a patient infected with Flaviviridae    comprising:    -   (a) administering an effective amount of a 2′-branched        nucleoside, such as β-D-2′-branched pyrimidine nucleoside, for        example β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine        ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        ββ-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof; optionally in a pharmaceutically acceptable carrier or        diluent;    -   (b) obtaining a viral sample from the patient;    -   (c) determining the replication fitness of the virus;    -   (d) determining whether the replication fitness of the virus in        the sample is less than the replication fitness of the wild-type        virus, which indicates resistance to the 2′-branched nucleoside,        such as β-D-2′-branched pyrimidine nucleoside, for example        β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine ester        prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof; and    -   (e) administering an effective amount of interferon to those        patients that are resistant to the 2′-branched nucleoside, such        as β-D-2′-branched pyrimidine nucleoside, for example        β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine ester        prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof.-   (ix) A method for treating a patient infected with Flaviviridae    comprising:    -   (a) administering an effective amount of a 2′-branched        nucleoside, such as β-D-2′-branched pyrimidine nucleoside, for        example β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine        ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof; optionally in a pharmaceutically acceptable carrier or        diluent;    -   (b) obtaining a viral culture sample from the patient;    -   (c) culturing the sample and comparing the plaque growth between        the sample and wild type virus;    -   (d) determining whether the plaque growth of the sample is        smaller than the plaque growth of the wildtype, which indicates        resistance to the 2′-branched nucleoside; and    -   (e) administering an effective amount of interferon to those        patients that are resistant to the 2′-branched nucleoside, such        as β-D-2′-branched pyrimidine nucleoside, for example        β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine ester        prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof.-   (x) A method for diagnosing the presence of a Flaviviridae resistant    to a 2′-branched nucleoside, such as β-D-2′-branched pyrimidine    nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as the    3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched    purine nucleoside, for example β-D-2′-CH₃-riboA or    β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the    3′-valine ester prodrug, or a pharmaceutically acceptable salt    thereof, in a patient comprising:    -   (a) obtaining a sample suspected of containing a Flaviviridae        nucleic acid sequence;    -   (b) contacting the sample with a detectable oligonucleotide        probe having a sequence complementary a codon that encodes a        serine in the highly conserved consensus sequence, XRXSGXXXT        (SEQ ID NO: 63), of domain B of the RNA polymerase region of        Flaviviridae (FIG. 11);    -   (b) allowing the probe to hybridize to the sequence; and    -   (c) detecting the hybridization of the probe the sequence to        determine the presence of a Flaviviridae resistant to the        2′-branched nucleoside, such as β-D-2′-branched pyrimidine        nucleoside, for example β-D-2′-CH₃-riboC or a prodrug, such as        the 3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a        β-D-2′-branched purine nucleoside, for example β-D-2′-CH₃-riboA        or β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as        the 3′-valine ester prodrug, or a pharmaceutically acceptable        salt thereof.-   (xi) A method for diagnosing of the presence of a Flaviviridae    resistant to the 2′-branched nucleoside, such as β-D-2′-branched    pyrimidine nucleoside, for example β-D-2′-CH₃-riboC or a prodrug,    such as the 3′-valine ester prodrug of β-D-2′-CH₃-riboC, or a    β-D-2′-branched purine nucleoside, for example β-D-2′-CH₃-riboA or    β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the    3′-valine ester prodrug, or a pharmaceutically acceptable salt    thereof, in a patient comprising:    -   (a) obtaining a sample suspected of containing a Flaviviridae        nucleic acid sequence;    -   (b) contacting the sample with a detectable oligonucleotide        probe having a sequence complementary to the cytidine at        nucleotide 1214 of the RNA polymerase region of BVDV or the        cytidine at nucleotide 8443 of HCV;    -   (b) allowing the probe to hybridize to the sequence; and    -   (c) detecting the hybridization of the probe to cytidine at        nucleotide 1214 of the RNA polymerase region of BVDV or at        nucleotide 8443 of HCV to determine the presence of a        Flaviviridae resistant to to the 2′-branched nucleoside, such as        β-D-2′-branched pyrimidine nucleoside, for example        β-D-2′-CH₃-riboC or a prodrug, such as the 3′-valine ester        prodrug of β-D-2′-CH₃-riboC, or a β-D-2′-branched purine        nucleoside, for example β-D-2′-CH₃-riboA or        β-D-2′-CH₃-ribo-6-N-methylaminopurine or a prodrug, such as the        3′-valine ester prodrug, or a pharmaceutically acceptable salt        thereof

The disclosed combination and/or alternation regimens are useful in theprevention and treatment of Flaviviridae infections, including BVDV,BDV, CSFV, DHF, yellow fever virus, shock syndrome, Japaneseencephalitis virus, and HCV.

In addition, the corresponding amino acid sequences of the Flaviviridaeviral markers diagnostic for long term response of Flaviviridae carriersto 2′-branched nucleoside therapy can be determined from theillustrative Flaviviridae nucleotide sequences.

In addition to identifying viral markers for the purposes of identifyingFlaviviridae strains that are associated with 2′-branched nucleosidefailure, the present invention can be utilized to also identifyFlaviviridae strains that respond to 2′-branched nucleoside therapy. Inthis respect, the absence of viral markers correlated with 2′-branchednucleoside therapy can be used to prescribe a course of treatment thatincludes 2′-branched nucleoside as a modality for those individuals thatcarrier Flaviviridae lacking viral markers correlated with 2′-branchednucleoside therapy failure.

In another embodiment, the invention provides an oligonucleotide primerfor amplifying an Flaviviridae nucleic acid sequence. In one embodiment,the oligonucleotide is at least 14 nucleotides in length and hybridizesunder sequence-specific, stringent hybridization conditions to anucleotide sequence that contains the marker correlated with therapyfailure.

Oligonucleotide sequences used as the hybridizing region of a primer canalso be used as the hybridizing region of a probe. Suitability of aprimer sequence for use as a probe depends on the hybridizationcharacteristics of the primer. Similarly, an oligonucleotide used as aprobe can be used as a primer.

Additionally, the invention provides a method, materials and a kit todetect proteins, peptides or peptide fragments that contain amino acids(as described extensively herein) that are predictive of the long termresponse of an Flaviviridae carrier to 2′-branched nucleoside therapy,or antibodies to those proteins, peptides or peptide fragments. Hostsera or tissue can be tested for either the protein or peptide or theantibody to the protein or peptide, depending on convenience and perhapsconcentration of the diagnostic material.

The protein, peptide or peptide fragment can be confirmed by reactionwith an antibody, preferably a monoclonal antibody, for example using aWestern blot method. Alternatively, the protein or peptide can beisolated and sequenced or otherwise identified by any means known in theart, including by 2D PAGE. In one embodiment, a reactive antibody bindsto an Flaviviridae protein or peptide sequence that includes a threoninerather than serine in the highly conserved consensus sequence, XRXSGXXXT(SEQ ID NO: 63), of domain B of the RNA polymerase region, for exampleat position 405 of the RNA polymerase region of BVDV genome or atposition 282 of the RNA polymerase region of the HCV genome.

In another embodiment, the reactive antibody binds specifically to apeptide sequence that includes a threonine rather than serine in thehighly conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), ofdomain B of the RNA polymerase region, for example at position 405 ofthe RNA polymerase region of BVDV genome or at position 282 of the RNApolymerase region of the HCV genome, which represent a specific pointmutations in the RNA polymerase region of Flaviviridae that iscorrelated with therapy failure.

In specific embodiments, an antibody is used that binds to at least onepeptide or peptide fragment encoded for by the nucleic acid sequences insequence ID Nos. 1-31.

In specific embodiments, an antibody is used that binds to at least onepeptide or peptide fragment encoded for by the nucleic acid sequences insequence ID Nos.32-62.

I. Definitions

As used herein, the term “resistant virus” refers to a virus thatexhibits a three, and more typically, five or greater fold increase inEC₅₀ compared to naive virus.

The term “amino acid” includes naturally occurring and synthetic α, γ orδ amino acids, and includes but is not limited to, amino acids found inproteins, i.e. glycine, alanine, valine, leucine, isoleucine,methionine, phenylalanine, tryptophan, proline, serine, threonine,cysteine, tyrosine, asparagine, glutamine, aspartate, glutamate, lysine,arginine and histidine. In a preferred embodiment, the amino acid is inthe L-configuration, but can also be in the D-configuration.Alternatively, the amino acid can be a derivative of alanyl, valinyl,leucinyl, isoleuccinyl, prolinyl, phenylalaninyl, tryptophanyl,methioninyl, glycinyl, serinyl, threoninyl, cysteinyl, tyrosinyl,asparaginyl, glutaminyl, aspartoyl, glutaroyl, lysinyl, argininyl,histidinyl, β-alanyl, β-valinyl, β-leucinyl, β-isoleuccinyl, β-prolinyl,β-phenylalaninyl, β-tryptophanyl, β-methioninyl, β-glycinyl, β-serinyl,β-threoninyl, β-cysteinyl, β-tyrosinyl, β-asparaginyl, β-glutaminyl,β-aspartoyl, β-glutaroyl, β-lysinyl, β-argininyl or β-histidinyl.

The abbreviations of amino acids used herein are described in Table 1.

TABLE 1 Amino Acids Codons Alanine Ala A GCA GCC GCG GCU Cysteine Cys CUGC UGU Aspartic Acid Asp D GAC GAU GAC GAU Glutamic Acid Glu E GAA GAGPhenylalanine Phe F UUC UUU Clycine Gly G GGA GCG GGG GGU Histidine HisH CAC CAU Isoleucine Ile I AUA AUC AUU Lysine Lys K AAA AAG Leucine LeuL UUA UUG CUA CUC CUG GUU Methionine Met M AUG Asparagine Asn N AAC AAUProline Pro P CCA CCC CCG CCU Glutamine Gln Q CAA CAG Arginine Arg RAGA AGG CGA CGC CGG CGU Serine Ser S AGC AGU UCA UCC UCG UCU ThreonineThr T ACA ACC ACG ACU Valine Val V GUA GUC GUG GUU Tryptophan Trp W UGGTyrosine Tyr Y UAC UAU

“Amplification reagents” refer to the various buffers, enzymes, primers,deoxynucleoside triphosphates (both conventional and unconventional),and primers used to perform the selected amplification procedure.

“Amplifying” or “Amplification”, which typically refers to an“exponential” increase in target nucleic acid, is being used herein todescribe both linear and exponential increases in the numbers of aselect target sequence of nucleic acid.

“Bind(s) substantially” refers to complementary hybridization between anoligonucleotide and a target sequence and embraces minor mismatches thatcan be accommodated by reducing the stringency of the hybridizationmedia to achieve the desired priming for the PCR polymerases ordetection of hybridization signal.

“Hybridizing” refers the binding of two single stranded nucleic acidsvia complementary base pairing.

“Nucleic acid” refers to a deoxyribonucleotide or ribonucleotide polymerin either single- or double-stranded form, and unless otherwise limited,would encompass known analogs of natural nucleotides that can functionin a similar manner as naturally occurring nucleotides.

“Nucleotide polymerases” refers to enzymes able to catalyze thesynthesis of DNA or RNA from nucleoside triphosphate precursors. Inamplification reactions, the polymerases are template-dependent andtypically add nucleotides to the 3′-end of the polymer being formed. Thepolymerase can be thermostable as described in U.S. Pat. Nos. 4,889,818and 5,079,352.

The term “oligonucleotide” refers to a molecule comprised of two or moredeoxyribonucleotides or ribonucleotides, such as primers, probes,nucleic acid fragments to be detected, and nucleic acid controls. Theexact size of an oligonucleotide depends on many factors and theultimate function or use of the oligonucleotide. Oligonucleotides can beprepared by any suitable method, including, for example, cloning andrestriction of appropriate sequences and direct chemical synthesis by amethod such as the phosphotriester method of Narang et al., Meth.Enzymol. 1979, 68:90-99; the phosphodiester method of Brown et al, Meth.Enzymol., 1979, 68:109-151; the diethylphosphoramidite method ofBeaucage et al., Tetrahedron Lett., 1981, 22:1859-1862; and the solidsupport method of U.S. Pat. No. 4,458,066.

The term “primer” refers to an oligonucleotide, whether natural orsynthetic, capable of acting as a point of initiation of DNA synthesisunder conditions in which synthesis of a primer extension productcomplementary to a nucleic acid strand is induced, i.e., in the presenceof four different nucleoside triphosphates and an agent forpolymerization (i.e., DNA polymerase or reverse transcriptase) in anappropriate buffer and at a suitable temperature. A primer is preferablya single-stranded oligodeoxyribonucleotide. The appropriate length of aprimer depends on the intended use of the primer but typically rangesfrom about 14 or about 15 to 25 or 30 nucleotides. Short primermolecules generally require cooler temperatures to form sufficientlystable hybrid complexes with the template. A primer need not reflect theexact sequence of the template but must be sufficiently complementary tohybridize with a template.

The term “primer” can refer to more than one primer, particularly in thecase where there is some ambiguity in the information regarding one orboth ends of the target region to be amplified. For instance, if aregion shows significant levels of polymorphism in a population,mixtures of primers can be prepared that will amplify alternatesequences. A primer can be labeled, if desired, by incorporating a labeldetectable by spectroscopic, photochemical, biochemical, immunochemical,or chemical means. For example, useful labels include ³²P, fluorescentdyes, electron-dense reagents, enzymes (as commonly used in an ELISA),biotin, or haptens and proteins for which antisera or monoclonalantibodies are available. A label can also be used to “capture” theprimer, so as to facilitate the immobilization of either the primer or aprimer extension product, such as amplified DNA, on a solid support.

“Probe” refers to an oligonucleotide which binds through complementarybase pairing to a subsequence of a target nucleic acid. It will beunderstood by one of skill in the art that probes will typicallysubstantially bind target sequences lacking complete complementaritywith the probe sequence depending upon the stringency of thehybridization conditions. The probes are preferably directly labeled aswith isotopes or indirectly labeled such as with biotin to which astreptavidin complex can later bind. By assaying for the presence orabsence of the probe, one can detect the presence or absence of thetarget.

“Subsequence” refers to a sequence of nucleic acids that comprise a partof a longer sequence of nucleic acids.

The term “target region” refers to a region of a nucleic acid to beanalyzed and can include a polymorphic region.

The term alkyl, as used herein, unless otherwise specified, refers to asaturated straight, branched, or cyclic, primary, secondary, or tertiaryhydrocarbon typically of C₁ to C₁₀, and specifically includes methyl,CF₃, CCl₃, CFCl₂, CF₂Cl, ethyl, CH₂CF₃, CF₂CF₃, propyl, isopropyl,cyclopropyl, butyl, isobutyl, t-butyl, pentyl, cyclopentyl, isopentyl,neopentyl, hexyl, isohexyl, cyclohexyl, cyclohexylmethyl,3-methylpentyl, 2,2-dimethylbutyl, and 2,3-dimethylbutyl. The termincludes both substituted and unsubstituted alkyl groups, andparticularly includes halogenated alkyl groups, and even moreparticularly fluorinated alkyl groups. Moieties with which the alkylgroup can be substituted are selected from the group consisting ofhalogen (fluoro, chloro, bromo or iodo), hydroxyl, amino, alkylamino,arylamino, alkoxy, aryloxy, nitro, cyano, sulfonic acid, sulfate,phosphonic acid, phosphate, or phosphonate, either unprotected, orprotected as necessary, as known to those skilled in the art, forexample, as taught in Greene, et al., Protective Groups in OrganicSynthesis, John Wiley and Sons, Second Edition, 1991, herebyincorporated by reference.

The term lower alkyl, as used herein, and unless otherwise specified,refers to a C₁ to C₄ saturated straight, branched, or if appropriate, acyclic (for example, cyclopropyl) alkyl group, including bothsubstituted and unsubstituted forms. Unless otherwise specificallystated in this application, when alkyl is a suitable moiety, lower alkylis preferred. Similarly, when alkyl or lower alkyl is a suitable moiety,unsubstituted alkyl or lower alkyl is preferred.

The term alkylamino or arylamino refers to an amino group that has oneor two alkyl or aryl substituents, respectively.

The term “protected” as used herein and unless otherwise defined refersto a group that is added to an oxygen, nitrogen, or phosphorus atom toprevent its further reaction or for other purposes. A wide variety ofoxygen and nitrogen protecting groups are known to those skilled in theart of organic synthesis.

The term aryl, as used herein, and unless otherwise specified, refers tophenyl, biphenyl, or naphthyl, and preferably phenyl. The term includesboth substituted and unsubstituted moieties. The aryl group can besubstituted with one or more moieties selected from the group consistingof halogen (fluoro, chloro, bromo or iodo), hydroxyl, amino, alkylamino,arylamino, alkoxy, aryloxy, nitro, cyano, sulfonic acid, sulfate,phosphonic acid, phosphate, or phosphonate, either unprotected, orprotected as necessary, as known to those skilled in the art, forexample, as taught in Greene, et al., Protective Groups in OrganicSynthesis, John Wiley and Sons, Second Edition, 1991.

The term alkaryl or alkylaryl refers to an alkyl group with an arylsubstituent. The term aralkyl or arylalkyl refers to an aryl group withan alkyl substituent.

The term halo, as used herein, includes chloro, bromo, iodo, and fluoro.

The term base refers to any purine or pyrimidine base including, but notlimited to, guanine, adenine, hypoxanthine, 2,6-diaminopurine,6-chloropurine, N⁶-alkylpurines, N⁶-acylpurines (wherein acyl isC(O)(alkyl, aryl, alkylaryl, or arylalkyl), N⁶-benzylpurine,N⁶-halopurine, N⁶-vinylpurine, N⁶-acetylenic purine, N⁶-acyl purine,N⁶-hydroxyalkyl purine, N⁶-thioalkyl purine, N²-alkylpurines,N²-alkyl-6-thiopurines, thymine, cytosine, 5-fluorocytosine,5-methylcytosine, 6-azapyrimidine, including 6-azacytosine, 2- and/or4-mercaptopyrmidine, uracil, 5-halouracil, including 5-fluorouracil,C⁵-alkylpyrimidines, C⁵-benzylpyrimidines, C⁵-halopyrimidines,C⁵-vinylpyrimidine, C⁵-acetylenic pyrimidine, C⁵-acyl pyrimidine,C⁵-hydroxyalkyl purine, C⁵-amidopyrimidine, C⁵-cyanopyrimidine,C⁵-nitropyrimidine, C⁵-amino-pyrimidine, N²-alkylpurines,N²-alkyl-6-thiopurines, 5-azacytidinyl, 5-aza-uracilyl,triazolopyridinyl, imidazolopyridinyl, pyrrolopyrimidinyl,pyrazolopyrimidinyl,

a base of the formula:

wherein:

-   -   G and L are each independently CH or N;    -   D is N, CH, C—CN, C—NO₂, C—C₁₋₃ alkyl, C—NHCONH₂, C—CONQ¹¹Q¹¹,        C—CSNQ¹¹Q¹¹, CCOOQ¹¹, C—C(═NH)NH₂, C-hydroxy, C—C₁₋₃alkoxy,        C-amino, C—C₁₋₄alkyl-amino, C-di(C₁₋₄ alkyl)amino, C-halogen,        C-(1,3-oxazol-2-yl), C-(1,3-thiazol-2-yl), or C-(imidazol-2-yl);        wherein alkyl is unsubstituted or substituted with one to three        groups independently selected from halogen, amino, hydroxy,        carboxy, and C₁₋₃ alkoxy;    -   E is N or CQ⁵;    -   W is O, S, or NR;    -   R is H, OH, alkyl;    -   Q⁶ is H, OH, SH, NH₂, C₁₋₄ alkylamino, di(C₁₋₄ alkyl)amino, C₃₋₆        cycloalkylamino, halogen,    -   C₁₋₄ alkyl, C₁₋₄ alkoxy, or CF₃;    -   Q⁵ is H, C₁₋₆ alkyl, C₂₋₆ alkenyl, C₂₋₆ alkynyl, C₁₋₄        alkylamino, CF₃, halogen, N, CN, NO₂, NHCONH₂, CONQ¹¹Q¹¹,        CSNQ¹¹Q¹¹, COOQ¹¹, C(═NH)NH₂, hydroxy, C₁₋₃alkoxy, amino, C₁₋₄        alkylamino, di(C₁₋₄ alkyl)amino, halogen, 1,3-oxazol-2-yl,        1,3-thiazol-2-yl, or imidazol-2-yl; wherein alkyl is        unsubstituted or substituted with one to three groups        independently selected from halogen, amino, hydroxy, carboxy,        and C₁₋₃ alkoxy;    -   Q⁷ and Q¹⁴ are each independently selected from the group        consisting of H, CF₃, OH, SH, OR, SR C₁₋₄ alkyl, amino, C₁₋₄        alkylamino, C₃₋₆ cycloalkylamino, and di(C₁₋₄ alkyl)amino;    -   Q¹¹ is independently H or C₁₋₆ alkyl;    -   Q⁸ is H, halogen, CN, carboxy, C₁₋₄ alkyloxycarbonyl, N₃, amino,        C₁₋₄ alkylamino, di(C₁₋₄ alkyl)amino, hydroxy, C₁₋₆ alkoxy, C₁₋₆        alkylthio, C₁₋₆ alkylsulfonyl, (C₁₋₄ alkyl)₀₋₂aminomethyl, NH₂,        CN, NO₂, C₁₋₃ alkyl, NHCONH₂, CONQ¹¹Q¹¹, CSNQ¹¹Q¹¹, COOQ¹¹,        C(═NH)NH₂, 1,3-oxazol-2-yl, 1,3-thiazol-2-yl, or imidazol-2-yl,        wherein alkyl is unsubstituted or substituted with one to three        groups independently selected from halogen, amino, hydroxy,        carboxy, and C₁₋₃ alkoxy;        a base of the formula:

wherein:

-   -   T₁ and T₂ are independently selected from N, CH, or C-Q¹⁶;    -   Q¹⁶, U, and Y are independently selected from is H, OH,        substituted or unsubstituted alkyl, substituted or unsubstituted        alkenyl, substituted or unsubstituted alkynyl, cycloalkyl,        CO-alkyl, CO-aryl, CO-alkoxyalkyl, chloro, bromo, fluoro, iodo,        OR⁴, NR⁴R⁵ or SR⁵, Br-vinyl, —O-alkyl, —O-alkenyl, —O-alkynyl,        —O-aryl, —O-aralkyl, —O-acyl, —O-cycloalkyl, NH₂, NH-alkyl,        N-dialkyl, NH-acyl, N-aryl, N-aralkyl, NH-cycloalkyl, SH,        S-alkyl, S-acyl, S-aryl, S-cycloalkyl, S-aralkyl, CN, N₃, COOH,        CONH₂, CO₂-alkyl, CONH-alkyl, CON-dialkyl, OH, CF₃, CH₂OH,        (CH₂)_(m)OH, (CH₂)_(m)NH₂, (CH₂)_(m)COOH, (CH₂)_(m)CN,        (CH₂)_(m)NO₂, (CH₂)_(m)CONH₂, C₁₋₄ alkylamino, di(C₁₋₄        alkyl)amino, C₃₋₆ cycloalkylamino, C₁₋₄ alkoxy, C₁₋₄        alkoxycarbonyl, C₁₋₆ alkylthio, C₁₋₆ alkylsulfonyl, (C₁₋₄        alkyl)₀₋₂aminomethyl, or —NHC(═NMNH₂;    -   R⁴ and R⁵ are independently selected from hydrogen, acyl        (including lower acyl), or alkyl (including but not limited to        methyl, ethyl, propyl and cyclopropyl);    -   m is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;    -   Z is S, SO, SO₂, C═O, or NQ²⁰;    -   Q²⁰ is H or alkyl; and    -   V₁ and V₂ are independently selected from CH or N;        a base of the formula:

wherein:

-   -   T₃ and T₄ are independently selected from N or CQ²²;    -   Q²² is independently selected from H, OH, substituted or        unsubstituted alkyl, substituted or unsubstituted alkenyl,        substituted or unsubstituted alkynyl, cycloalkyl, CO-alkyl,        CO-aryl, CO-alkoxyalkyl, chloro, bromo, fluoro, iodo, OR⁴, NR⁴R⁵        or SR⁵, Br-vinyl, —O-alkyl, —O-alkenyl, —O-alkynyl, —O-aryl,        —O-aralkyl, —O-acyl, —O-cycloalkyl, NH₂, NH-alkyl, N-dialkyl,        NH-acyl, N-aryl, N-aralkyl, NH-cycloalkyl, SH, S-alkyl, S-acyl,        S-aryl, S-cycloalkyl, S-aralkyl, CN, N₃, COOH, CONH₂, CO₂-alkyl,        CONH-alkyl, CON-dialkyl, OH, CF₃, CH₂OH, (CH₂)_(m)OH,        (CH₂)_(m)NH₂, (CH₂)_(m)COOH, (CH₂)_(m)CN, (CH₂)_(m)NO₂,        (CH₂)_(m)CONH₂, C₁₋₄ alkylamino, di(C₁₋₄ alkyl)amino, C₃₋₆        cycloalkylamino, C₁₋₄ alkoxy, C₁₋₄ alkoxycarbonyl, C₁₋₆        alkylthio, C₁₋₆ alkylsulfonyl, (C₁₋₄ alkyl)₀₋₂aminomethyl, or        —NHC(═NH)NH₂;    -   T₅ is NH;    -   R⁴ and R⁵ are independently selected from hydrogen, acyl        (including lower acyl), or alkyl (including but not limited to        methyl, ethyl, propyl and cyclopropyl);    -   m is 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10;    -   T₆, T₇, T₈, T₉, T₁₀, T₁₁, and T₁₂ are independently selected        from N or CH;    -   U₂ is H, straight chained, branched or cyclic alkyl, CO-alkyl,        CO-aryl, CO-alkoxyalkyl, chloro, bromo, fluoro, iodo, OR⁴, NR⁴R⁵        or SR⁵;    -   Y₂ is O, S, NH, NR or CQ²⁴Q²⁶ where R is H, OH, or alkyl;    -   Q²⁴ and Q²⁶ are independently selected from H, alkyl, straight        chained, branched or cyclic alkyl, CO-alkyl, CO-aryl,        CO-alkoxyalkyl, chloro, bromo, fluoro, iodo, OR⁴, NR⁴R⁵ or SR⁵.

Further examples of purine bases include, but are not limited to,guanine, adenine, hypoxanthine, 2,6-diaminopurine, 6-chloropurine, and6-N-methylamino purine. Functional oxygen and nitrogen groups on thebase can be protected as necessary or desired. Suitable protectinggroups are well known to those skilled in the art, and includetrimethylsilyl, dimethylhexylsilyl, t-butyldimethylsilyl, andt-butyldiphenylsilyl, trityl, alkyl groups, and acyl groups such asacetyl and propionyl, methanesulfonyl, and p-toluenesulfonyl.

The term acyl or O-linked ester refers to a group of the formula C(O)R′,wherein R′ is an straight, branched, or cyclic alkyl (including loweralkyl), amino acid, aryl including phenyl, alkaryl, aralkyl includingbenzyl, alkoxyalkyl including methoxymethyl, aryloxyalkyl such asphenoxymethyl; or substituted alkyl (including lower alkyl), arylincluding phenyl optionally substituted with chloro, bromo, fluoro,iodo, C₁ to C₄ alkyl or C₁ to C₄ alkoxy, sulfonate esters such as alkylor aralkyl sulphonyl including methanesulfonyl, the mono, di ortriphosphate ester, trityl or monomethoxy-trityl, substituted benzyl,alkaryl, aralkyl including benzyl, alkoxyalkyl including methoxymethyl,aryloxyalkyl such as phenoxymethyl. Aryl groups in the esters optimallycomprise a phenyl group. In particular, acyl groups include acetyl,trifluoroacetyl, methylacetyl, cyclopropylacetyl, propionyl, butyryl,hexanoyl, heptanoyl, octanoyl, neo-heptanoyl, phenylacetyl,2-acetoxy-2-phenylacetyl, diphenylacetyl,α-methoxy-α-trifluoromethyl-phenylacetyl, bromoacetyl,2-nitro-benzeneacetyl, 4-chloro-benzeneacetyl,2-chloro-2,2-diphenylacetyl, 2-chloro-2-phenylacetyl, trimethylacetyl,chlorodifluoroacetyl, perfluoroacetyl, fluoroacetyl,bromodifluoroacetyl, methoxyacetyl, 2-thiopheneacetyl,chlorosulfonylacetyl, 3-methoxyphenylacetyl, phenoxyacetyl,tert-butylacetyl, trichloroacetyl, monochloro-acetyl, dichloroacetyl,7H-dodecafluoro-heptanoyl, perfluoro-heptanoyl,7H-dodeca-fluoroheptanoyl, 7-chlorododecafluoro-heptanoyl,7-chloro-dodecafluoro-heptanoyl, 7H-dodecafluoroheptanoyl,7H-dodeca-fluoroheptanoyl, nona-fluoro-3,6-dioxa-heptanoyl,nonafluoro-3,6-dioxaheptanoyl, perfluoroheptanoyl, methoxybenzoyl,methyl 3-amino-5-phenylthiophene-2-carboxyl,3,6-dichloro-2-methoxy-benzoyl, 4-(1,1,2,2-tetrafluoro-ethoxy)-benzoyl,2-bromo-propionyl, omega-aminocapryl, decanoyl, n-pentadecanoyl,stearyl, 3-cyclopentyl-propionyl, 1-benzene-carboxyl, O-acetylmandelyl,pivaloyl acetyl, 1-adamantane-carboxyl, cyclohexane-carboxyl,2,6-pyridinedicarboxyl, cyclopropane-carboxyl, cyclobutane-carboxyl,perfluorocyclohexyl carboxyl, 4-methylbenzoyl, chloromethylisoxazolylcarbonyl, perfluorocyclohexyl carboxyl, crotonyl,1-methyl-1H-indazole-3-carbonyl, 2-propenyl, isovaleryl,1-pyrrolidinecarbonyl, 4-phenylbenzoyl.

As used herein, the term “substantially free of” or “substantially inthe absence of” refers to a nucleoside composition that includes atleast 95% to 98% by weight, and even more preferably 99% to 100% byweight, of the designated enantiomer of that nucleoside. In a preferredembodiment, in the methods and compounds of this invention, thecompounds are substantially free of enantiomers.

Similarly, the term “isolated” refers to a nucleoside composition thatincludes at least 95% to 98% by weight, and even more preferably 99% to100% by weight, of the nucleoside, the remainder comprising otherchemical species or enantiomers.

The term host, as used herein, refers to an unicellular or multicellularorganism in which the virus can replicate, including cell lines andanimals, and preferably a human. Alternatively, the host can be carryinga part of the Flaviviridae viral genome, whose replication or functioncan be altered by the compounds of the present invention. The term hostspecifically refers to infected cells, cells transfected with all orpart of the Flaviviridae genome and animals, in particular, primates(including chimpanzees) and humans. In most animal applications of thepresent invention, the host is a human patient. Veterinary applications,in certain indications, however, are clearly anticipated by the presentinvention (such as chimpanzees).

II. 2′-Branched Nucleosides and Prodrugs Thereof

In the broadest embodiment, the present invention provides a method totreat a Flavivirdae infection that is resistant to a 2′-branchednucleoside. In one embodiment, the 2′-branched nucleoside is a purine,or a purine derivative such as a pyrrolo-purine. In a preferredembodiment, the 2′-branched nucleoside is a pyrimidine. Othersub-embodiments include the 2′-alkyl and 2′-methyl-branched pyrimidinenucleosides, including the 2′-branched uracil and 2′-branched cytosinenucleosides. In another embodiment, the 2′-branched nucleoside is apurine. Other sub-embodiments include the 2′-alkyl and2′-methyl-branched purine nucleosides, including the 2′-branchedadenosine nucleosides and the 2′-branched 6-N-methylamino purinenucleosides.

In a specific embodiment, the 2′-branched pyrimidine nucleoside isrepresented by the compound β-D-2′-CH₃-riboC, which is represented bythe formula:

wherein R³ is H, phosphate (including mono-, di- or triphosphate and astabilized phosphate prodrug); acyl (including lower acyl); alkyl(including lower alkyl); sulfonate ester (including alkyl or arylalkylsulfonyl including methanesulfonyl); benzyl, wherein the phenyl group isoptionally substituted with one or more substituents as described in thedefinition of aryl given herein; lipid (including a phospholipid); aminoacid; carbohydrate; peptide; cholesterol; or a pharmaceuticallyacceptable leaving group that provides a compound wherein R³ is H orphosphate when administered in vivo.

In another specific embodiment, the 2′-branched purine nucleoside isrepresented by the compound β-D-2′-CH₃-ribo-6-N-methylaminopurine, whichis represented by the formula:

wherein R³ is H, phosphate (including mono-, di- or triphosphate and astabilized phosphate prodrug); acyl (including lower acyl); alkyl(including lower alkyl); sulfonate ester (including alkyl or arylalkylsulfonyl including methanesulfonyl); benzyl, wherein the phenyl group isoptionally substituted with one or more substituents as described in thedefinition of aryl given herein; lipid (including a phospholipid); aminoacid; carbohydrate; peptide; cholesterol; or a pharmaceuticallyacceptable leaving group that provides a compound wherein R³ is H orphosphate when administered in vivo.

In one embodiment of the invention, the 2′-branched nucleoside is of thegeneral formula:

or its pharmaceutically acceptable prodrug and/or salt, wherein

-   R¹, R², and R³ are independently H, phosphate (including mono-, di-    or triphosphate and a stabilized phosphate prodrug); acyl (including    lower acyl); alkyl (including lower alkyl); sulfonate ester    (including alkyl or arylalkyl sulfonyl including methanesulfonyl);    benzyl, wherein the phenyl group is optionally substituted with one    or more substituents as described in the definition of aryl given    herein; lipid (including a phospholipid); amino acid; carbohydrate;    peptide; cholesterol; or a pharmaceutically acceptable leaving group    that provides a compound wherein R¹, R² or R³ is independently H or    phosphate when administered in vivo; and-   R⁴ is hydrogen, hydroxy, alkyl (including lower alkyl), azido,    cyano, alkenyl, alkynyl, Br-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), chloro, bromo, fluoro, iodo, NO₂, NH₂, —NH(lower    alkyl), —NH(acyl), —N(lower alkyl)₂, or —N(acyl)₂;    and Base is a purine or pyrimidine as further described herein.

In another embodiment of the invention, the 2′-branched nucleoside is ofthe general formula:

or its pharmaceutically acceptable prodrug and/or salt, whereinBase is a purine or pyrimidine base as defined herein;

-   R¹, R² and R³ are independently H, phosphate (including mono-, di-    or triphosphate and a stabilized phosphate); straight chained,    branched or cyclic alkyl (including lower alkyl); acyl (including    lower acyl); CO-alkyl, CO-aryl, CO-alkoxyalkyl, CO-aryloxyalkyl,    CO-substituted aryl, sulfonate ester (including alkyl or arylalkyl    sulfonyl including methanesulfonyl); benzyl, wherein the phenyl    group is optionally substituted with one or more substituents as    described in the definition of aryl given herein; alkylsulfonyl,    arylsulfonyl, aralkylsulfonyl, lipid (including a phospholipid);    amino acid; carbohydrate; peptide; cholesterol; or a    pharmaceutically acceptable leaving group that provides a compound    wherein R¹, R² or R³ is independently H or phosphate when    administered in vivo;-   R⁶ is alkyl (including lower alkyl and halogenated alkyl), CH₃, CF₃,    azido, cyano, alkenyl, alkynyl, Br-vinyl, 2-Br-ethyl, —C(O)O(alkyl),    —C(O)O(lower alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower    alkyl), —O(alkenyl), CF₃, chloro, bromo, fluoro, iodo, NO₂, NH₂,    —NH(lower alkyl), —NH(acyl), —N(lower alkyl)₂, —N(acyl)₂; and-   R⁷ is hydrogen, OR³, hydroxy, alkyl (including lower alkyl), azido,    cyano, alkenyl, alkynyl, Br-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), fluorine, chlorine, bromine, iodine, NO₂, NH₂,    —NH(lower alkyl), —NH(acyl), —N(lower alkyl)₂, —N(acyl)₂; and-   X is O, S, SO₂ or CH₂.    and Base is a purine or pyrimidine as further described herein.

In yet another embodiment the invention, the 2′-branched nucleoside isof the general formula:

wherein:Base is a purine or pyrimidine base as defined herein;

-   R⁶ is alkyl (including lower alkyl and halogenated alkyl), CH₃, CF₃,    azido, cyano, alkenyl, alkynyl, Br-vinyl, 2-Br-ethyl, —C(O)O(alkyl),    —C(O)O(lower alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower    alkyl), —O(alkenyl), CF₃, fluoro, chloro, bromo, iodo, NO₂, NH₂,    —NH(lower alkyl), —NH(acyl), —N(lower alkyl)₂, —N(acyl)₂;-   R⁷ is OR², hydroxy, alkyl (including lower alkyl), azido, cyano,    alkenyl, alkynyl, Br-vinyl, halo-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), fluorine, chlorine, bromine, iodine, NO₂, NH₂,    —NH(lower alkyl), —NH(acyl), —N(lower alkyl)₂, —N(acyl)₂;-   R⁹ is hydrogen, OR³, hydroxy, alkyl (including lower alkyl), azido,    cyano, alkenyl, alkynyl, Br-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), chlorine, bromine, iodine, NO₂, NH₂, —NH(lower alkyl),    —NH(acyl), —N(lower alkyl)₂, —N(acyl)₂;-   R¹⁰ is H, alkyl (including lower alkyl), fluorine, chlorine, bromine    or iodine;-   R¹, R² and R³ are independently H, phosphate (including mono-, di-    or triphosphate and a stabilized phosphate); straight chained,    branched or cyclic alkyl (including lower alkyl); acyl (including    lower acyl); CO-alkyl, CO-aryl, CO-alkoxyalkyl, CO-aryloxyalkyl,    CO-substituted aryl, sulfonate ester (including alkyl or arylalkyl    sulfonyl including methanesulfonyl); benzyl, wherein the phenyl    group is optionally substituted with one or more substituents as    described in the definition of aryl given herein; alkylsulfonyl,    arylsulfonyl, aralkylsulfonyl, lipid (including a phospholipid);    amino acid; carbohydrate; peptide; cholesterol; or a    pharmaceutically acceptable leaving group that provides a compound    wherein R¹, R² or R³ is independently H or phosphate when    administered in vivo; and-   X is O, S, SO₂ or CH₂.    General Synthesis of 2′-Branched Nucleosides:    1. Glycosylation of the Nucleobase with an Appropriately Modified    Sugar

The key starting material for this process can be an appropriatelysubstituted sugar with a 2′-OH and 2′-H, with the appropriate leavinggroup (LG), for example an acyl group or a chloro, bromo, fluoro oriodo. The sugar can be purchased or can be prepared by any known meansincluding standard epimerization, substitution, oxidation and reductiontechniques. The substituted sugar can then be oxidized with theappropriate oxidizing agent in a compatible solvent at a suitabletemperature to yield the 2′-modified sugar. Possible oxidizing agentsare Jones reagent (a mixture of chromic acid and sulfuric acid),Collins's reagent (dipyridine Cr(VI) oxide, Corey's reagent (pyridiniumchlorochromate), pyridinium dichromate, acid dichromate, potassiumpermanganate, MnO₂, ruthenium tetroxide, phase transfer catalysts suchas chromic acid or permanganate supported on a polymer, Cl₂-pyridine,H₂O₂-ammonium molybdate, NaBrO₂-CAN, NaOCl in HOAc, copper chromite,copper oxide, Raney nickel, palladium acetate, Meerwin-Pondorf-Verleyreagent (aluminum t-butoxide with another ketone) andN-bromosuccinimide.

Then coupling of an organometallic carbon nucleophile, such as aGrignard reagent, an organolithium, lithium dialkylcopper or R⁴—SiMe₃(wherein R⁴ is defined below) in TBAF with the ketone with theappropriate non-protic solvent at a suitable temperature, yields the2′-alkylated sugar. The alkylated sugar can be optionally protected witha suitable protecting group, preferably with an acyl or silyl group, bymethods well known to those skilled in the art, as taught by Greene etal. Protective Groups in Organic Synthesis, John Wiley and Sons, SecondEdition, 1991.

The optionally protected sugar can then be coupled to the BASE bymethods well known to those skilled in the art, as taught by TownsendChemistry of Nucleosides and Nucleotides, Plenum Press, 1994. Forexample, an acylated sugar can be coupled to a silylated base with alewis acid, such as tin tetrachloride, titanium tetrachloride ortrimethylsilyltriflate in the appropriate solvent at a suitabletemperature. Alternatively, a halo-sugar can be coupled to a silylatedbase with the presence of trimethylsilyltriflate.

Subsequently, the nucleoside can be deprotected by methods well known tothose skilled in the art, as taught by Greene et al. Protective Groupsin Organic Synthesis, John Wiley and Sons, Second Edition, 1991.

In a particular embodiment, the 2′-C-branched ribonucleoside is desired.The synthesis of a ribonucleoside is shown in Scheme 1. Alternatively,the deoxyribo-nucleoside can be used. To obtain these nucleosides, theformed ribonucleoside can optionally be protected by methods well knownto those skilled in the art, as taught by Greene et al. ProtectiveGroups in Organic Synthesis, John Wiley and Sons, Second Edition, 1991,and then the 2′-OH can be reduced with a suitable reducing agent.Optionally, the 2′-hydroxyl can be activated to facilitate reduction;i.e. via the Barton reduction.

wherein:LG is a leaving group;

-   R¹, R², and R³ are independently H, phosphate (including mono-, di-    or triphosphate and a stabilized phosphate prodrug); acyl (including    lower acyl); alkyl (including lower alkyl); sulfonate ester    (including alkyl or arylalkyl sulfonyl including methanesulfonyl);    benzyl, wherein the phenyl group is optionally substituted with one    or more substituents as described in the definition of aryl given    herein; lipid (including a phospholipid); amino acid; carbohydrate;    peptide; cholesterol; or a pharmaceutically acceptable leaving group    that provides a compound wherein R¹, R² or R³ is independently H or    phosphate when administered in vivo; and-   R⁴ is hydrogen, hydroxy, alkyl (including lower alkyl), azido,    cyano, alkenyl, alkynyl, Br-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), chloro, bromo, fluoro, iodo, NO₂, NH₂, —NH(lower    alkyl), —NH(acyl), —N(lower alkyl)₂, or —N(acyl)₂.    2. Modification of a Pre-Formed Nucleoside

The key starting material for this process can be an appropriatelysubstituted nucleoside with a 2′-OH and 2′-H. The nucleoside can bepurchased or can be prepared by any known means including standardcoupling techniques. The nucleoside can be optionally protected withsuitable protecting groups, preferably with acyl or silyl groups, bymethods well known to those skilled in the art, as taught by Greene etal. Protective Groups in Organic Synthesis, John Wiley and Sons, SecondEdition, 1991.

The appropriately protected nucleoside can then be oxidized with theappropriate oxidizing agent in a compatible solvent at a suitabletemperature to yield the 2′-modified sugar. Possible oxidizing agentsare Jones reagent (a mixture of chromic acid and sulfuric acid),Collins's reagent (dipyridine Cr(VI) oxide, Corey's reagent (pyridiniumchlorochromate), pyridinium dichromate, acid dichromate, potassiumpermanganate, MnO₂, ruthenium tetroxide, phase transfer catalysts suchas chromic acid or permanganate supported on a polymer, Cl₂-pyridine,H₂O₂-ammonium molybdate, NaBrO₂-CAN, NaOCl in HOAc, copper chromite,copper oxide, Raney nickel, palladium acetate, Meerwin-Pondorf-Verleyreagent (aluminum t-butoxide with another ketone) andN-bromosuccinimide.

Subsequently, the nucleoside can be deprotected by methods well known tothose skilled in the art, as taught by Greene et al. Protective Groupsin Organic Synthesis, John Wiley and Sons, Second Edition, 1991.

In a particular embodiment, the 2′-C-branched ribonucleoside is desired.The synthesis of a ribonucleoside is shown in Scheme 2. Alternatively,deoxyribo-nucleoside can be used. To obtain these nucleosides, theformed ribonucleoside can optionally be protected by methods well knownto those skilled in the art, as taught by Greene et al. ProtectiveGroups in Organic Synthesis, John Wiley and Sons, Second Edition, 1991,and then the 2′-OH can be reduced with a suitable reducing agent.Optionally, the 2′-hydroxyl can be activated to facilitate reduction;i.e. via the Barton reduction.

wherein:

-   R¹ and R³ are independently H, phosphate (including mono-, di- or    triphosphate and a stabilized phosphate prodrug); acyl (including    lower acyl); alkyl (including lower alkyl); sulfonate ester    (including alkyl or arylalkyl sulfonyl including methanesulfonyl);    benzyl, wherein the phenyl group is optionally substituted with one    or more substituents as described in the definition of aryl given    herein; lipid (including a phospholipid); amino acid; carbohydrate;    peptide; cholesterol; or a pharmaceutically acceptable leaving group    that provides a compound wherein R¹ or R³ is independently H or    phosphate when administered in vivo; and-   R⁴ is hydrogen, hydroxy, alkyl (including lower alkyl), azido,    cyano, alkenyl, alkynyl, Br-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), chloro, bromo, fluoro, iodo, NO₂, NH₂, —NH(lower    alkyl), —NH(acyl), —N(lower alkyl)₂, or —N(acyl)₂.    General Synthesis of 2′-Branched Pyrimidine Nucleoside    1. Glycosylation of the Pyrimidine with an Appropriately Modified    Sugar

A representative general method for the preparation of 2′-branchedpyrimidine nucleoside is outlined in Scheme 3. This scheme illustratesthe 2′branched pyrimidine nucleoside in the β-D-ribo configuration.Alternatively, one skilled in the art could modify the general scheme toproduce 2′-β-L-pyrimidine nucleoside. The key starting material for thisprocess can be an appropriately substituted sugar with a 2′-OH and 2′-H,with the appropriate leaving group (LG), for example an acyl group or achloro, bromo, fluoro or iodo. The sugar can be purchased or can beprepared by any known means including standard epimerization,substitution, oxidation and reduction techniques. The substituted sugarcan then be oxidized with the appropriate oxidizing agent in acompatible solvent at a suitable temperature to yield the 2′-modifiedsugar. Possible oxidizing agents are Jones reagent (a mixture of chromicacid and sulfuric acid), Collins's reagent (dipyridine Cr(VI) oxide,Corey's reagent (pyridinium chlorochromate), pyridinium dichromate, aciddichromate, potassium permanganate, MnO₂, ruthenium tetroxide, phasetransfer catalysts such as chromic acid or permanganate supported on apolymer, Cl₂-pyridine, H₂O₂-ammonium molybdate, NaBrO₂-CAN, NaOCl inHOAc, copper chromite, copper oxide, Raney nickel, palladium acetate,Meerwin-Pondorf-Verley reagent (aluminum t-butoxide with another ketone)and N-bromosuccinimide.

Then coupling of an organometallic carbon nucleophile, such as aGrignard reagent, an organolithium, lithium dialkylcopper or R⁴—SiMe₃ inTBAF with the ketone with the appropriate non-protic solvent at asuitable temperature, yields the 2′-alkylated sugar. The alkylated sugarcan be optionally protected with a suitable protecting group, preferablywith an acyl or silyl group, by methods well known to those skilled inthe art, as taught by Greene et al. Protective Groups in OrganicSynthesis, John Wiley and Sons, Second Edition, 1991.

The optionally protected sugar can then be coupled to a prymidine baseby methods well known to those skilled in the art, as taught by TownsendChemistry of Nucleosides and Nucleotides, Plenum Press, 1994. Forexample, an acylated sugar can be coupled to a silylated pyrimidine,such as cytidine, with a lewis acid, such as tin tetrachloride, titaniumtetrachloride or trimethylsilyltriflate in the appropriate solvent at asuitable temperature. Alternatively, a halo-sugar can be coupled to asilylated pyrimidine, such as a cytidine, with the presence oftrimethylsilyltriflate.

wherein:

-   R¹, R², and R³ are independently H, phosphate (including mono-, di-    or triphosphate and a stabilized phosphate prodrug); acyl (including    lower acyl); alkyl (including lower alkyl); sulfonate ester    (including alkyl or arylalkyl sulfonyl including methanesulfonyl);    benzyl, wherein the phenyl group is optionally substituted with one    or more substituents as described in the definition of aryl given    herein; lipid (including a phospholipid); amino acid; carbohydrate;    peptide; cholesterol; or a pharmaceutically acceptable leaving group    that provides a compound wherein R¹, R² or R³ is independently H or    phosphate when administered in vivo; and-   R⁴ is hydrogen, hydroxy, alkyl (including lower alkyl), azido,    cyano, alkenyl, alkynyl, Br-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), chloro, bromo, fluoro, iodo, NO₂, NH₂, —NH(lower    alkyl), —NH(acyl), —N(lower alkyl)₂, or —N(acyl)₂.    2. Modification of a Pre-Formed 2′-Branched Pyrimidine Nucleoside

The key starting material for this process can be an appropriatelysubstituted 2′-branched pyrimidine nucleoside with a 2′-OH and 2′-H. The2′-branched pyrimidine nucleoside can be purchased or can be prepared byany known means including standard coupling techniques. The 2′-branchedpyrimidine nucleoside can be optionally protected with suitableprotecting groups, preferably with acyl or silyl groups, by methods wellknown to those skilled in the art, as taught by Greene et al. ProtectiveGroups in Organic Synthesis, John Wiley and Sons, Second Edition, 1991.

The appropriately protected 2′-branched pyrimidine nucleoside can thenbe oxidized with the appropriate oxidizing agent in a compatible solventat a suitable temperature to yield the 2′-modified sugar. Possibleoxidizing agents are Jones reagent (a mixture of chromic acid andsulfuric acid), Collins's reagent (dipyridine Cr(VI) oxide, Corey'sreagent (pyridinium chlorochromate), pyridinium dichromate, aciddichromate, potassium permanganate, MnO₂, ruthenium tetroxide, phasetransfer catalysts such as chromic acid or permanganate supported on apolymer, Cl₂-pyridine, H₂O₂-ammonium molybdate, NaBrO₂—CAN, NaOCl inHOAc, copper chromite, copper oxide, Raney nickel, palladium acetate,Meerwin-Pondorf-Verley reagent (aluminum t-butoxide with another ketone)and N-bromosuccinimide.

Subsequently, the 2′-branched pyrimidine nucleoside can be deprotectedby methods well known to those skilled in the art, as taught by Greeneet al. Protective Groups in Organic Synthesis, John Wiley and Sons,Second Edition, 1991.

In a particular embodiment, the 2′-C-branched ribonucleoside is desired.The synthesis of a ribonucleoside is shown in Scheme 4. Alternatively,deoxyribo-nucleoside can be used. To obtain these nucleosides, theformed ribonucleoside can optionally be protected by methods well knownto those skilled in the art, as taught by Greene et al. ProtectiveGroups in Organic Synthesis, John Wiley and Sons, Second Edition, 1991,and then the 2′-OH can be reduced with a suitable reducing agent.Optionally, the 2′-hydroxyl can be activated to facilitate reduction;i.e. via the Barton reduction.

wherein:

-   R¹ and R³ are independently H, phosphate (including mono-, di- or    triphosphate and a stabilized phosphate prodrug); acyl (including    lower acyl); alkyl (including lower alkyl); sulfonate ester    (including alkyl or arylalkyl sulfonyl including methanesulfonyl);    benzyl, wherein the phenyl group is optionally substituted with one    or more substituents as described in the definition of aryl given    herein; lipid (including a phospholipid); amino acid; carbohydrate;    peptide; cholesterol; or a pharmaceutically acceptable leaving group    that provides a compound wherein R¹ or R³ is independently H or    phosphate when administered in vivo; and-   R⁴ is hydrogen, hydroxy, alkyl (including lower alkyl), azido,    cyano, alkenyl, alkynyl, Br-vinyl, —C(O)O(alkyl), —C(O)O(lower    alkyl), —O(acyl), —O(lower acyl), —O(alkyl), —O(lower alkyl),    —O(alkenyl), chloro, bromo, fluoro, iodo, NO₂, NH₂, —NH(lower    alkyl), —NH(acyl), —N(lower alkyl)₂, or —N(acyl)₂.    General Synthesis of 2′-Branched Purine Nucleoside    1. Glycosylation of the Pyrimidine with an Appropriately Modified    Sugar

A representative general method for the preparation of 2′-branchedpurine nucleoside is outlined in Scheme 5 below. This scheme illustratesthe synthesis of 2′-branched purine nucleoside in the β-D-riboconfiguration. Alternative, it is well appreciated to those skilled inthe art are able to prepare the β-L-ribo configuration using theappropriate starting material. The starting material is a 3,5-bisprotected alkyl furanoside, such as methyl furanoside, of structuralformula (i). The C-2 hydroxyl group is then oxidized with a suitableoxidizing agent, such as a chromium trioxide or chromate reagent orDess-Martin periodinane, or by Swern oxidation, to afford a C-2 ketoneof structural formula (ii). Addition of a Grignard reagent, such as analkyl, alkenyl, or alkynyl magnesium halide (for example, MeMgBr,EtMgBr, vinylMgBr, allylMgBr, and ethynylMgBr) or an alkyl, alkenyl, oralkynyl lithium, such as MeLi, across the carbonyl double bond of (ii)in a suitable organic solvent, such as tetrahydrofuran, diethyl ether,and the like, affords the C-2 tertiary alcohol of structural formula(iii). A good leaving group (such as F, Cl, Br, and I) is nextintroduced at the C-1 (anorneric) position of the furanose sugarderivative by treatment of the furanoside of formula (iii) with ahydrogen halide in a suitable organic solvent, such as hydrogen bromidein acetic acid, to afford the intermediate furanosyl halide (iv). AC-sulfonate, such as methanesulfonate (MeSO₂O—),trifluoromethanesulfonate (CF₃SO₂O—) or p-toluenesulfonate (—OTs), mayalso serve as a useful leaving group in the subsequent reaction togenerate the glycosidic (nucleosidic) linkage. The nucleosidic linkageis constructed by treatment of the intermediate of structural formula(iv) with the metal salt (such as lithium, sodium, or potassium) of anappropriately substituted 1H-pyrrolo[2,3-d]pyrimidine (v), such as anappropriately substituted 4-halo-IH-pyrrolo[2,3-d]pyrimidine, which canbe generated in situ by treatment with an alkali hydride (such as sodiumhydride), an alkali hydroxide (such as potassium hydroxide), an alkalicarbonate (such as potassium carbonate), or an alkalihexamethyldisilazide (such as NaHMDS) in a suitable anhydrous organicsolvent, such as acetonitrile, tetrahydrofuran,1-methyl-2-pyrrolidinone, or N,N-dimethyl-formamide (DMF). Thedisplacement reaction can be catalyzed by using a phase-transfercatalyst, such as TDA-1 or triethylbenzylammonium chloride, in atwo-phase system (solid-liquid or liquid-liquid). The optionalprotecting groups in the protected nucleoside of structural formula (vi)are then cleaved following established deprotection methodologies, suchas those described in T. W. Greene and P. G. M. Wuts, “Protective Groupsin Organic Synthesis,” P ed., John Wiley & Sons, 1999. Optionalintroduction of an amino group at the 4-position of thepyrrolo[2,3-d]pyrimidine nucleus is effected by treatment of the 4-halointermediate (vi) with the appropriate amine, such as alcoholic ammoniaor liquid ammonia, to generate a primary amine at the C-4 position(—NH₂), an alkylamine to generate a secondary amine (—NHR), or adialkylamine to generate a tertiary amine (—NRR′). A7H-pyrrolo[2,3-d]pyrimidin-4(3H) one compound may be derived byhydrolysis of (vi) with aqueous base, such as aqueous sodium hydroxide.Alcoholysis (such as methanolysis) of 1-6 affords a C-4 alkoxide (—OR),whereas treatment with an alkyl mercaptide affords a C-4 alkylthio (—SR)derivative. Subsequent chemical manipulations well-known topractitioners of ordinary skill in the art of organic/medicinalchemistry may be required to attain the desired compounds of the presentinvention.

wherein:

-   P¹ and P² are independently a protecting group; alternatively, P′    and P² can come together to form a cyclic protecting group;-   R⁵ and R⁶ are independently alkyl group;-   M is Li, Na, or K;-   X¹ and X² are independently F, Cl, Br, or I;-   R⁷, R⁸, and R⁹ are independently hydrogen, hydroxyl, halogen,    alkoxy, amino, alkylamino, or alkyl.    Synthesis of β-D-2′-CH₃-riboC

The following syntheses provided are non-limiting steps to achieve thecompound β-D-2′-CH₃-riboC. One of ordinary skill in the art may modifythe synthesis in any known manner to achieve the compoundβ-D-2′-CH₃-riboC.

1. Glycosylation of the Nucleobase with an Appropriately Modified Sugar

The key starting material for this process can be an appropriatelysubstituted sugar with a 2′-OH and 2′-H, with the appropriate leavinggroup (LG), for example an acyl group or a chloro, bromo, fluoro oriodo. The sugar can be purchased or can be prepared by any known meansincluding standard epimerization, substitution, oxidation and reductiontechniques. The substituted sugar can then be oxidized with theappropriate oxidizing agent in a compatible solvent at a suitabletemperature to yield the 2′-modified sugar. Possible oxidizing agentsare Jones reagent (a mixture of chromic acid and sulfuric acid),Collins's reagent (dipyridine Cr(VI) oxide, Corey's reagent (pyridiniumchlorochromate), pyridinium dichromate, acid dichromate, potassiumpermanganate, MnO₂, ruthenium tetroxide, phase transfer catalysts suchas chromic acid or permanganate supported on a polymer, Cl₂-pyridine,H₂O₂-ammonium molybdate, NaBrO₂—CAN, NaOCl in HOAc, copper chromite,copper oxide, Raney nickel, palladium acetate, Meerwin-Pondorf-Verleyreagent (aluminum t-butoxide with another ketone) andN-bromosuccinimide.

Then coupling of an organometallic carbon nucleophile, such as aGrignard reagent, an organolithium, lithium dialkylcopper or CH₃—SiMe₃in TBAF with the ketone with the appropriate non-protic solvent at asuitable temperature, yields the 2′-methyl sugar. The methyl sugar canbe optionally protected with a suitable protecting group, preferablywith an acyl or silyl group, by methods well known to those skilled inthe art, as taught by Greene et al. Protective Groups in OrganicSynthesis, John Wiley and Sons, Second Edition, 1991.

The optionally protected sugar can then be coupled to the BASE bymethods well known to those skilled in the art, as taught by TownsendChemistry of Nucleosides and Nucleotides, Plenum Press, 1994. Forexample, an acylated sugar can be coupled to a silylated base with alewis acid, such as tin tetrachloride, titanium tetrachloride ortrimethylsilyltriflate in the appropriate solvent at a suitabletemperature. Alternatively, a halo-sugar can be coupled to a silylatedbase with the presence of trimethylsilyltriflate.

Subsequently, the 2′-methyl-nucleoside can be deprotected by methodswell known to those skilled in the art, as taught by Greene et al.Protective Groups in Organic Synthesis, John Wiley and Sons, SecondEdition, 1991.

The synthesis of a 2′-methyl-nucleoside is shown in Scheme 6.

wherein:

-   LG is a leaving group; and-   R¹, R², and R³ are independently H, phosphate (including mono-, di-    or triphosphate and a stabilized phosphate prodrug); acyl (including    lower acyl); alkyl (including lower alkyl); sulfonate ester    (including alkyl or arylalkyl sulfonyl including methanesulfonyl);    benzyl, wherein the phenyl group is optionally substituted with one    or more substituents as described in the definition of aryl given    herein; lipid (including a phospholipid); amino acid; carbohydrate;    peptide; cholesterol; or a pharmaceutically acceptable leaving group    that provides a compound wherein R¹, R² or R³ is independently H or    phosphate when administered in vivo.    2. Modification of a Pre-Formed 2′-Methyl Nucleoside

The key starting material for this process can be an appropriatelysubstituted 2% methyl-cytidine nucleoside with a 2′-OH and 2′-H. Thenucleoside can be purchased or can be prepared by any known meansincluding standard coupling techniques. The nucleoside can be optionallyprotected with suitable protecting groups, preferably with acyl or silylgroups, by methods well known to those skilled in the art, as taught byGreene et al. Protective Groups in Organic Synthesis, John Wiley andSons, Second Edition, 1991.

The appropriately protected 2′-methyl-cytidine nucleoside can then beoxidized with the appropriate oxidizing agent in a compatible solvent ata suitable temperature to yield the 2′-methyl sugar. Possible oxidizingagents are Jones reagent (a mixture of chromic acid and sulfuric acid),Collins's reagent (dipyridine Cr(VI) oxide, Corey's reagent (pyridiniumchlorochromate), pyridinium dichromate, acid dichromate, potassiumpermanganate, MnO₂, ruthenium tetroxide, phase transfer catalysts suchas chromic acid or permanganate supported on a polymer, Cl₂-pyridine,H₂O₂-ammonium molybdate, NaBrO₂—CAN, NaOCl in HOAc, copper chromite,copper oxide, Raney nickel, palladium acetate, Meerwin-Pondorf-Verleyreagent (aluminum t-butoxide with another ketone) andN-bromosuccinimide.

Subsequently, the nucleoside can be deprotected by methods well known tothose skilled in the art, as taught by Greene et al. Protective Groupsin Organic Synthesis, John Wiley and Sons, Second Edition, 1991.

The synthesis of a 2′-methyl-cytidine nucleoside is shown in Scheme 7.

wherein:

-   R¹ and R³ are independently H, phosphate (including mono-, di- or    triphosphate and a stabilized phosphate prodrug); acyl (including    lower acyl); alkyl (including lower alkyl); sulfonate ester    (including alkyl or arylalkyl sulfonyl including methanesulfonyl);    benzyl, wherein the phenyl group is optionally substituted with one    or more substituents as described in the definition of aryl given    herein; lipid (including a phospholipid); amino acid; carbohydrate;    peptide; cholesterol; or a pharmaceutically acceptable leaving group    that provides a compound wherein R¹ or R³ is independently H or    phosphate when administered in vivo.    Pharmaceutically Acceptable Prodrugs

The term “pharmaceutically acceptable prodrug and/or salt” is usedthroughout the specification to describe any pharmaceutically acceptableform (such as an ester, phosphate ester, salt of an ester or a relatedgroup) of a nucleoside compound which, upon administration to a patient,provides the parent nucleoside compound. Pharmaceutically acceptablesalts include those derived from pharmaceutically acceptable inorganicor organic bases and acids. Suitable salts include those derived fromalkali metals such as potassium and sodium, alkaline earth metals suchas calcium and magnesium, among numerous other acids well known in thepharmaceutical art. Pharmaceutically acceptable prodrugs refer to acompound that is metabolized, for example hydrolyzed or oxidized, in thehost to form the compound of the present invention. Typical examples ofprodrugs include compounds that have biologically labile protectinggroups on a functional moiety of the active compound. Prodrugs includecompounds that can be oxidized, reduced, aminated, deaminated,hydroxylated, dehydroxylated, hydrolyzed, dehydrolyzed, alkylated,dealkylated, acylated, deacylated, phosphorylated, dephosphorylated toproduce the active compound. The compounds of this invention possessantiviral activity against a Flaviviridae, or are metabolized to acompound that exhibits such activity.

2′-Branched nucleosides, including 2′-branched pyrimidine nucleoside,such as β-D-2′-CH₃-riboC, or related compounds administered as acylatedor nucleoside prodrugs can be used in combination or alternationtherapy.

Any of the nucleosides described herein or other compounds that containa hydroxyl or amine function can be administered as a nucleoside prodrugto increase the activity, bioavailability, stability or otherwise alterthe properties of the nucleoside. A number of nucleoside prodrug ligandsare known. In general, alkylation, acylation or other lipophilicmodification of the hydroxyl group of the compound or of the mono, di ortriphosphate of the nucleoside will increase the stability of thenucleoside. Examples of substituent groups that can replace one or morehydrogens on the phosphate moiety or hydroxyl are alkyl, aryl, steroids,carbohydrates, including sugars, 1,2-diacylglycerol and alcohols. Manyare described in R. Jones and N. Bischofberger, Antiviral Research, 27(1995) 1-17. Any of these can be used in combination with the disclosednucleosides or other compounds to achieve a desire effect

The active nucleoside or other hydroxyl containing compound can also beprovided as an ether lipid (and particularly a 5′-ether lipid for anucleoside), as disclosed in the following references: Kucera, L. S., N.Iyer, E. Leake, A. Raben, Modest E. K., D. L. W., and C. Piantadosi.1990. “Novel membrane-interactive ether lipid analogs that inhibitinfectious HIV-1 production and induce defective virus formation.” AIDSRes. Hum. Retro Viruses. 6:491-501; Piantadosi, C., J. Marasco C. J., S.L. Morris-Natschke, K. L. Meyer, F. Gumus, J. R. Surles, K. S. Ishaq, L.S. Kucera, N. Iyer, C. A. Wallen, S. Piantadosi, and E. J. Modest. 1991.“Synthesis and evaluation of novel ether lipid nucleoside conjugates foranti-HIV activity.” J. Med. Chem. 34:1408.1414; Hosteller, K. Y., D. D.Richman, D. A. Carson, L. M. Stuhmiller, G. M. T. van Wijk, and H. vanden Bosch. 1992. “Greatly enhanced inhibition of human immunodeficiencyvirus type 1 replication in CEM and HT4-6C cells by 3′-deoxythymidinediphosphate dimyristoylglycerol, a lipid prodrug of 3,-deoxythymidine.”Antimicrob. Agents Chemother. 36:2025.2029; Hostetler, K. Y., L. M.Stuhmiller, H. B. Lenting, H. van den Bosch, and D. D. Richman, 1990.“Synthesis and antiretroviral activity of phospholipid analogs ofazidothymidine and other antiviral nucleosides.” J. Biol. Chem.265:61127. Nonlimiting examples of U.S. patents that disclose suitablelipophilic substituents that can be covalently incorporated into thenucleoside or other hydroxyl or amine containing compound, preferably atthe 5′-OH position of the nucleoside or lipophilic preparations, includeU.S. Pat. No. 5,149,794 (Sep. 22, 1992, Yatvin et al.); U.S. Pat. No.5,194,654 (Mar. 16, 1993, Hostetler et al., U.S. Pat. No. 5,223,263(Jun. 29, 1993, Hostetler et al.); U.S. Pat. No. 5,256,641 (Oct. 26,1993, Yatvin et al.); U.S. Pat. No. 5,411,947 (May 2, 1995, Hostetler etal.); U.S. Pat. No. 5,463,092 (Oct. 31, 1995, Hostetler et al.); U.S.Pat. No. 5,543,389 (Aug. 6, 1996, Yatvin et al.); U.S. Pat. No.5,543,390 (Aug. 6, 1996, Yatvin et al.); U.S. Pat. No. 5,543,391 (Aug.6, 1996, Yatvin et al.); and U.S. Pat. No. 5,554,728 (Sep. 10, 1996;Basava et al.), all of which are incorporated herein by reference.Foreign patent applications that disclose lipophilic substituents thatcan be attached to the nucleosides of the present invention, orlipophilic preparations, include WO 89/02733, WO 90/00555, WO 91/16920,WO 91/18914, WO 93/00910, WO 94/26273, WO 96/15132, EP 0 350 287, EP93917054.4, and WO 91/19721.

2′, 3′ and 5′-Prodrugs of 2′-branched β-D nucleosides, or theirpharmaceutically acceptable salts or pharmaceutically acceptableformulations containing these compounds can be used to treatFlaviviridae infections. Specifically, the 3′-valine ester prodrug ofβ-D-2′-CH₃-riboC represented by the formula:

or its pharmaceutically acceptable salt, can be administered to asubject for the treatment of a Flaviviridae infection.

In one embodiment, 2′-branched β-D nucleoside 2′-prodrug includesbiologically cleavable moieties at the 2′ and/or 5′ positions. Preferredmoieties are natural or synthetic D or L amino acid esters, including Dor L-valyl, though preferably L-amino acid esters, such as L-valyl, andalkyl esters including acetyl. Therefore, this invention specificallyincludes 2′-D or L-amino acid ester and 2′,5′-D or L-diamino acid ester,preferably L-amino acid ester, of 2′-branched β-D or β-L nucleosideswith any desired purine or pyrimidine base, wherein the parent drugoptionally has an EC₅₀ of less than 15 micromolar, and even morepreferably less than 10 micromolar; 2′-(alkyl or aryl)ester or2′,5′-di(alkyl or aryl)ester of 2′-branched β-D or β-L nucleosides withany desired purine or pyrimidine base, wherein the parent drugoptionally has an EC₅₀ of less than 10 or 15 micromolar; and prodrugs of2′,5′-diesters of 2′-branched β-D or β-L nucleosides wherein (i) the 2′ester is a natural or synthetic D or L-amino acid ester, thoughpreferably an L-amino acid ester, and the 5′-ester is an alkyl or arylester; (ii) both esters are independently natural or synthetic D orL-amino acid ester, though preferably both are L-amino acid esters;(iii) both esters are independently alkyl or aryl esters; and (iv) the2′ ester is independently an alkyl or aryl ester and the 5′-ester is anatural or synthetic D or L-amino acid ester, though preferably anL-amino acid ester, wherein the parent drug optionally has an EC₅₀ ofless than 10 or 15 micromolar.

Examples of prodrugs falling within the invention are 2′-D or L-valineester of β-D-2′-methyl-cytidine; β-D-2′,6-dimethyl-cytidine; 2′-L-valineester of β-D-2′,6-dimethyl-thymidine; 2′-L-valine ester ofβ-D-2′,8-dimethyl-adenosine; 2′-L-valine ester ofβ-D-2′,8-dimethyl-guanosine; 2′-L-valine ester ofβ-D-2′,6-dimethyl-5-fluorocytidine; 2′-L-valine ester ofβ-D-2′,6-dimethyl-uridine; 2′-acetyl ester ofβ-D-2′,6-dimethyl-cytidine; 2′-acetyl ester ofβ-D-2′,6-dimethyl-thymidine; 2′-acetyl esterβ-D-2′,8-dimethyl-adenosine; 2′-acetyl ester ofβ-D-2′,8-dimethyl-guanosine; 2′-acetyl ester ofβ-D-2′,6-dimethyl-5-fluoro-cytidine; and 2′-esters ofβ-D-2′,6-dimethyl-(cytidine, 5-fluorocytidine, uridine or thymidine) or2′-esters of β-D-2′-methyl-cytidine or β-D-2′,8-dimethyl-(guanosine,adenosine or inosine) wherein (i) the 2′ ester is an amino acid ester;or (ii) the 2′ ester is an alkyl or aryl ester.

Additional examples of prodrugs falling within the invention are2′,5′-L-divaline ester of β-D-2′-methyl cytidine;β-D-2′,6-dimethyl-cytidine (dival-2′,6-diMe-L-dC); 2′,5′-L-divalineester of β-D-2′,6-dimethyl-thymidine; 2′,5′-L-divaline ester ofβ-D-2′,8-dimethyl-adenosine; 2′,5′-L-divaline ester ofβ-D-2′,8-dimethyl-guanosine; 2′,5′-L-divaline ester ofβ-D-2′,6-dimethyl-5-fluoro-cytidine; 2′,5′-L-divaline ester ofβ-D-2′,6-dimethyl-uridine; 2′,5′-diacetyl ester ofβ-D-2′,6-dimethyl-cytidine; 2′,5′-diacetyl ester ofβ-D-2′,6-dimethyl-thymidine; 2′,5′-diacetyl ester ofβ-D-2′,8-dimethyl-adenosine; 2′,5′-diacetyl ester ofβ-D-2′,8-dimethyl-guanosine; 2′,5′-diacetyl ester ofβ-D-2′,6-dimethyl-5-fluoro-cytidine; and 2′,5′-diesters ofβ-D-2′,6-dimethyl-(cytidine, 5-fluoro-cytidine, uridine or thymidine) or2′,5′-diesters of β-D-2′-methyl cytidine orβ-D-2′,8-dimethyl-(guanosine, adenosine or inosine) wherein (i) the 2′ester is an amino acid ester and the 5′-ester is an alkyl or aryl ester;(ii) both esters are amino acid esters; (iii) both esters areindependently alkyl or aryl esters; or (iv) the 2′ ester is an alkyl oraryl ester and the 5′-ester is an amino acid ester.

In another embodiment, the 2′-branched β-D nucleoside 3′-prodrugincludes biologically cleavable moieties at the 3′ and/or 5′ positions.Preferred moieties are natural or synthetic D or L amino acid esters,such as valyl, though preferably L-amino acids, such as L-valyl, andalkyl esters including acetyl. Therefore, this invention specificallyincludes 3′-L-amino acid ester and 3′,5′-L-diamino acid ester of a2′-branched β-D or β-L nucleosides with any desired purine or pyrimidinebase, wherein the parent drug optionally has an EC₅₀ of less than 15micromolar, and even more preferably less than 10 micromolar; 3′-(alkylor aryl) ester or 3′,5′-L-di(alkyl or aryl) ester of 2′-branched β-D orβ-L nucleosides with any desired purine or pyrimidine base, wherein theparent drug optionally has an EC₅₀ of less than 10 or 15 micromolar; andprodrugs of 3′,5′-diesters of 2′-branched β-D or β-L nucleosides wherein(i) the 3′ ester is a natural or synthetic D or L amino acid ester andthe 5′-ester is an alkyl or aryl ester; (ii) both esters are natural orsynthetic D or L-amino acid esters; (iii) both esters are independentlyalkyl or aryl esters; and (iv) the 3′ ester is independently an alkyl oraryl ester and the 5′-ester is a natural or synthetic D or L-amino acidester, wherein the parent drug optionally has an EC₅₀ of less than 10 or15 micromolar.

Examples of prodrugs falling within the invention are 3′-L-valine esterof β-D-2′-methyl-cytidine; β-D-2′,6-dimethyl-cytidine; 3′-L-valine esterof β-D-2′,6-dimethyl-thymidine; 3′-L-valine ester ofβ-D-2′,8-dimethyl-adenosine; 3′-L-valine ester ofβ-D-2′,8-dimethyl-guanosine; 3′-L-valine ester ofβ-D-2′,6-dimethyl-5-fluorocytidine; 3′-L-valine ester ofβ-D-2′,6-dimethyl-uridine; 3′-acetyl ester ofβ-D-2′,6-dimethyl-cytidine; 3′-acetyl ester ofβ-D-2′,6-dimethyl-thymidine; 3′-acetyl ester ofβ-D-2′,8-dimethyl-adenosine; 3′-acetyl ester ofβ-D-2′,8-dimethyl-guanosine; 3′-acetyl ester of β-D-2′-methyl-cytidine;3′-acetyl ester of β-D-2′,6-dimethyl-5-fluoro-cytidine; and 3′-esters ofβ-D-2′,6-dimethyl-(cytidine, 5-fluorocytidine, uridine or thymidine) or3′-esters of β-D-2′,8-dimethyl-(guanosine, adenosine or inosine) wherein(i) the 3′ ester is an amino acid ester; or (ii) the 3′ ester is analkyl or aryl ester.

Additional examples of prodrugs falling within the invention are3′,5′-L-divaline ester of of β-D-2′-methyl-cytidine;β-D-2′,6-dimethyl-cytidine (dival-2′,6-diMe-L-dC); 3′,5′-L-divalineester of β-D-2′,6-dimethyl-thymidine; 3′,5′-L-divaline ester ofβ-D-2′,8-dimethyl-adenosine; 3′,5′-L-divaline ester ofβ-D-2′,8-dimethyl-guanosine; 3′,5′-L-divaline ester ofβ-D-2′,6-dimethyl-5-fluoro-cytidine; 3′,5′-L-divaline ester ofβ-D-2′,6-dimethyl-uridine; 3′,5′-diacetyl ester ofβ-D-2′,6-dimethyl-cytidine; 3′,5′-diacetyl ester ofβ-D-2′,6-dimethyl-thymidine; 3′,5′-diacetyl ester ofβ-D-2′,8-dimethyl-adenosine; 3′,5′-diacetyl ester ofβ-D-2′,8-dimethyl-guanosine; 3′,5′-diacetyl ester ofβ-D-2′,6-dimethyl-5-fluoro-cytidine; and 3′,5′-diesters ofβ-D-2′,6-dimethyl-(cytidine, 5-fluoro-cytidine, orβ-D-2′-methyl-cytidine, uridine or thymidine) or 3′,5′-diesters ofβ-D-2′,8-dimethyl-(guanosine, adenosine or inosine) wherein (i) the 3′ester is an amino acid ester and the 5′-ester is an alkyl or aryl ester;(ii) both esters are amino acid esters; (iii) both esters areindependently alkyl or aryl esters; or (iv) the 3′ ester is an alkyl oraryl ester and the 5′-ester is an amino acid ester.

In another embodiment, the prodrug of 2′-branched β-D nucleosideincludes biologically cleavable moieties at the 2′, 3′ and/or 5′positions. Preferred moieties are natural or synthetic D or L amino acidesters, including D or L-valyl, though preferably L-amino acid esters,such as L-valyl, and alkyl esters including acetyl. Therefore, thisinvention specifically includes 2′,3′-L or D-diamino acid ester and2′,3′,5′-L or D-triamino acid ester of 2′-branched β-D or β-Lnucleosides, preferably L-amino acid, with any desired purine orpyrimidine base, wherein the parent drug optionally has an EC₅₀ of lessthan 15 micromolar, and even more preferably less than 10 micromolar;2′,3′-di(alkyl or aryl)ester or 2′,3′,5′-L-tri(alkyl or aryl) ester of2′-branched β-D or β-L nucleosides with any desired purine or pyrimidinebase, wherein the parent drug optionally has an EC₅₀ of less than 10 or15 micromolar; and prodrugs of 2′,3′-diesters of 2′-branched β-D or β-Lnucleosides wherein (i) the 2′ ester is an amino acid ester and the3′-ester is an alkyl or aryl ester; (ii) both esters are amino acidesters; (iii) both esters are independently alkyl or aryl esters; and(iv) the 2′ ester is independently an alkyl or aryl ester and the3′-ester is an amino acid ester, wherein the parent drug optionally hasan EC₅₀ of less than 10 or 15 micromolar. Further, 2′,3′,5′-triesters of2′-branched β-D or β-L nucleosides wherein (i) all three esters areamino acid esters; (ii) all three esters are independently alkyl or arylesters; (iii) the 2′ ester is an amino acid ester, the 3′ ester is anamino acid ester and the 5′-ester is an alkyl or aryl ester; (iv) the 2′ester is an amino acid ester, the 3′ ester is an alkyl or aryl ester andthe 5′-ester is an alkyl or aryl ester; (v) the 2′ ester is an alkyl oraryl ester, the 3′ ester is an alkyl or aryl ester and the 5′-ester isan amino acid ester; (vi) the 2′ ester is an alkyl or aryl ester, the 3′ester is an amino acid ester and the 5′-ester is an amino acid ester;(vii) the 2′ ester is an alkyl or aryl ester, the 3′ ester is an aminoacid ester and the 5′-ester is an alkyl or aryl ester; and (viii) the 2′ester is an amino acid ester, the 3′ ester is an alkyl or aryl ester andthe 5′-ester is an amino acid ester; wherein the parent drug optionallyhas an EC₅₀ of less than 10 or 15 micromolar.

Examples of prodrugs falling within the invention include2′,3′-L-divaline ester of β-D-2′-methyl-cytidine;β-D-2′,6-dimethyl-cytidine (dival-2′,6-diMe-L-dC); 2′,3′-L-divalineester of β-D-2′,6-dimethyl-thymidine; 2′,3′-L-divaline ester ofβ-D-2′,8-dimethyl-adenosine; 2′,3′-L-divaline ester ofβ-D-2′,8-dimethyl-guanosine; 2′,3′-L-divaline ester ofβ-D-2′,6-dimethyl-5-fluoro-cytidine; 2′,3′-L-divaline ester ofβ-D-2′,6-dimethyl-uridine; 2′,3′-diacetyl ester ofβ-D-2′,6-dimethyl-cytidine; 2′,3′-diacetyl ester ofβ-D-2′,6-dimethyl-thymidine; 2′,3′-diacetyl ester ofβ-D-2′,8-dimethyl-adenosine; 2′,3′-diacetyl of β-D-2′-methyl-cytidine;2′,3′-diacetyl ester of β-D-2′,8-dimethyl-guanosine; 2′,3′-diacetylester of β-D-2′,6-dimethyl-5-fluoro-cytidine; and 2′,3′-diesters ofβ-D-2′,6-dimethyl-(cytidine, 5-fluorocytidine, uridine or thymidine) or2′,3′-diesters of β-D-2′,8-dimethyl-(guanosine, adenosine or inosine)wherein (i) the 2′ ester is an amino acid ester and the 3′-ester is analkyl or aryl ester; (ii) both esters are amino acid esters; (iii) bothesters are independently alkyl or aryl esters; or (iv) the 2′ ester isan alkyl or aryl ester and the 3′-ester is an amino acid ester.

Additional examples of prodrugs falling within the invention include2′,3′,5′-L-trivaline ester of β-D-2′-methyl-cytidine;β-D-2′,6-dimethyl-cytidine (trival-2′,6-diMe-L-dC); 2′,3′,5′-L-trivalineester of β-D-2′,6-dimethyl-thymidine; 2′,3′,5′-L-trivaline ester ofβ-D-2′,8-dimethyl-adenosine; 2′,3′,5′-L-trivaline ester ofβ-D-2′,8-dimethyl-guanosine; 2′,3′,5′-L-trivaline ester ofβ-D-2′,6-dimethyl-5-fluoro-cytidine; 2′,3′,5′-L-trivaline ester ofβ-D-2′,6-dimethyl-uridine; 2′,3′,5′-triacetyl ester ofβ-D-2′,6-dimethyl-cytidine; 2′,3′,5′-triacetyl ester ofβ-D-2′,6-dimethyl-thymidine; 2′,3′,5′-triacetyl ester ofβ-D-2′,8-dimethyl-adenosine; 2′,3′,5′-triacetyl ester ofβ-D-2′,8-dimethyl-guanosine; 2′,3′,5′-triacetyl ester ofβ-D-2′,6-dimethyl-5-fluoro-cytidine; and 2′,3′,5′-triesters ofβ-D-2′,6-dimethyl-(cytidine, 5-fluorocytidine, uridine or thymidine) and2′,3′,5′-triesters of β-D-2′,8-dimethyl-(guanosine, adenosine orinosine) wherein (i) all three esters are amino acid esters; (ii) allthree esters are independently alkyl or aryl esters; (iii) the 2′ esteris an amino acid ester, the 3′ ester is an amino acid ester and the5′-ester is an alkyl or aryl ester; (iv) the 2′ ester is an amino acidester, the 3′ ester is an alkyl or aryl ester and the 5′-ester is analkyl or aryl ester; (v) the 2′ ester is an alkyl or aryl ester, the 3′ester is an alkyl or aryl ester and the 5′-ester is an amino acid ester;(vi) the 2′ ester is an alkyl or aryl ester, the 3′ ester is an aminoacid ester and the 5′-ester is an amino acid ester; (vii) the 2′ esteris an alkyl or aryl ester, the 3′ ester is an amino acid ester and the5′-ester is an alkyl or aryl ester; and (viii) the 2′ ester is an aminoacid ester, the 3′ ester is an alkyl or aryl ester and the 5′-ester isan amino acid ester.

Further examples of prodrugs falling within the invention includeprodrugs disclosed in U.S. Pat. Nos. 6,284,748 and 6,312,662. Inparticular, the prodrugs of the present invention include compounds ofthe structure

wherein:

-   V, W and W′ are independently selected from the group consisting of    —H, alkyl, aralkyl, alicyclic, aryl, substituted aryl, heteroaryl,    substituted heteroaryl, 1-alkenyl, and 1-alkynyl; or-   together V and Z are connected via an additional 3-5 atoms to form a    cyclic group containing 5-7 atoms, optionally 1 heteroatom,    substituted with hydroxy, acyloxy, alkoxycarbonyloxy, or    aryloxycarbonyloxy attached to a carbon atom that is three atoms    from both O groups attached to the phosphorus; or-   together V and Z are connected via an additional 3-5 atoms to form a    cyclic group, optionally containing 1 heteroatom, that is fused to    an aryl group at the beta and gamma position to the O attached to    the phosphorus; or-   together V and W are connected via an additional 3 carbon atoms to    form an optionally substituted cyclic group containing 6 carbon    atoms and substituted with one substituent selected from the group    consisting of hydroxy, acyloxy, alkoxycarbonyloxy,    alkylthiocarbonyloxy, and aryloxycarbonyloxy, attached to one of    said carbon atoms that is three atoms from an O attached to the    phosphorus;-   together Z and W are connected via an additional 3-5 atoms to form a    cyclic group, optionally containing one heteroatom, and V must be    aryl, substituted aryl, heteroaryl, or substituted heteroaryl;-   together W and W′ are connected via an additional 2-5 atoms to form    a cyclic group, optionally containing 0-2 heteroatoms, and V must be    aryl, substituted aryl, heteroaryl, or heteroaryl;-   Z is selected from the group consisting of —CHR²OH, —CHR²OC(O)R³,    —CHR²OC(S)R³, —CHR²OC(S)OR³, —CHR²OC(O)SR³, —CHR²OCO₂R³, —OR², —SR²,    —CHR²N₃, —CH₂aryl, —CH(aryl)OH, —CH(CH═CR² ₂)OH, —CH(C≡CR²)OH, —R²,    —NR² ₂, —OCOR³, —OCO₂R³, —SCOR³, —SCO₂R³, —NHCOR², —NHCO₂R³,    —CH₂NHaryl, —(CH₂)_(p)—OR¹², and —(CH₂)_(p)—SR¹²;-   p is an integer 2 or 3;-   R² is selected from the group consisting of R.sup.3 and —H;-   R³ is selected from the group consisting of alkyl, aryl, alicyclic,    and aralkyl;-   R¹² is selected from the group consisting of —H, and lower acyl;-   M is selected from the group that attached to PO₃ ²⁻, P₂O₆ ³⁻ or    P₃O₉ ⁴⁻ is a the 2′-branched nucleoside, and is attached to the    phosphorus via a carbon, oxygen, sulfur or nitrogen atom.

In one non-limiting example, the prodrug is attached to the nucleosideas in the following compounds

General Synthesis of 2′ and/or 3′-Prodrugs

The key starting material for this process is an appropriatelysubstituted 2′-branched β-D nucleosides. The branched nucleoside can bepurchased or can be prepared by any known means including the techniquesdisclosed herein. The branched nucleoside can be optionally protectedwith a suitable protecting group, preferably with a silyl group, bymethods well known to those skilled in the art, as taught by Greene etal. Protective Groups in Organic Synthesis, John Wiley and Sons, SecondEdition, 1991. The protected branched nucleoside can then be coupledwith a suitable acyl doner, such as an acyl chloride and/or an acylanhydride with the appropriate protic or aprotic solvent at a suitabletemperature, to give the 2′ and/or 3′ prodrug of 2′-branched β-Dnucleoside. Alternatively, the protected branched nucleoside can then becoupled with a suitable acyl, such as a carboxylic acid, such asalkanoic acid and/or amino acid residue, optionally with a suitablecoupling agent, with the appropriate aprotic solvent at a suitabletemperature, to give the 2′ and/or 3′ prodrug of 2′-branched β-Dnucleoside. Possible coupling reagents are any reagents that promotecoupling, including but are not limiting to, Mitsunobu reagents (e.g.diisopropyl azodicarboxylate and diethyl azodicarboxylate) withtriphenylphosphine or various carbodiimides.

For example, simple amino-alcohols can be esterified using acidchlorides in refluxing acetonitrile-benzene mixture (See Scheme 8 below:Synthetic Communications, 1978, 8(5), 327-333; hereby incorporated byreference). Alternatively, esterification can be achieved using ananhydride, as described in J. Am. Chem. Soc., 1999, 121(24), 5661-5664.

III. Detection of the β-D-2′-CH₃-riboC Induced Mutation in aFlaviviridae Genome

In one embodiment, a method is provided for treating a patient infectedwith Flaviviridae comprising:

-   -   (i) administering an effective amount of β-D-2′-CH₃-riboC or a        prodrug, such as the 3′ valine ester prodrug of        β-D-2′-CH₃-riboC, or a pharmaceutically acceptable salt thereof;    -   (ii) identifying viral resistance to β-D-2′-CH₃-riboC in the        patient;    -   (iii) administering an effective amount of one or more drugs        that in combination and/or alternation with one or more drugs        that directly or indirectly induce a mutation in a Flaviviridae        at a location other than a mutation of a nucleotide that results        in a change from serine to a different amino acid in the highly        conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of        domain B of the RNA polymerase region, and/or one or more drugs        that are associated with such a mutation.

In another embodiment, a method is provided for treating a patientinfected with HCV comprising:

-   -   (i) administering an effective amount of β-D-2′-CH₃-riboC or a        prodrug, such as the 3′ valine ester prodrug of        β-D-2′-CH₃-riboC, or a pharmaceutically acceptable salt thereof;    -   (ii) identifying viral resistance to β-D-2′-CH₃-riboC in the        patient;    -   (iii) administering an effective amount of one or more drugs        that directly or indirectly induce a mutation in a Flaviviridae        at a location other than a mutation of a nucleotide that results        in a change from serine at position 282 to a different amino        acid, such as threonine, in the highly conserved consensus        sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B of the RNA        polymerase region, and/or one or more drugs that is associated        with such a mutation.

In one embodiment, a method is provided for treating a host infectedwith BVDV comprising:

-   -   (i) administering an effective amount of β-D-2′-CH₃-riboC or a        prodrug, such as the 3′ valine ester prodrug of        β-D-2′-CH₃-riboC, or a pharmaceutically acceptable salt thereof;    -   (ii) identifying viral resistance to β-D-2′-CH₃-riboC in the        host;    -   (iii) administering an effective amount of one or more drugs        that directly or indirectly induce a mutation in a Flaviviridae        at a location other than a mutation of a nucleotide that results        in a change from serine at position 405 to a different amino        acid, such as threonine, in the highly conserved consensus        sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B of the RNA        polymerase region, and/or one or more drugs that is associated        with such a mutation.

In another embodiment, the invention provides a method for treating apatient infected with Flaviviridae comprising:

-   -   (i) administering an effective amount of β-D-2′-CH₃-riboC or a        prodrug, such as the 3′ valine ester prodrug of        β-D-2′-CH₃-riboC, or a pharmaceutically acceptable salt thereof;    -   (ii) identifying viral resistance to β-D-2′-CH₃-riboC in the        patient;    -   (iii) administering an effective amount of interferon.

In certain embodiments, identification of viral resistance toβ-D-2′-CH₃-riboC in the patient can be determined by a phenotypicanalysis of viral plaque growth. In another embodiment, identificationof viral resistance to β-D-2′-CH₃-riboC in the patient can be determinedby the replication fitness of the virus. In a further embodiment,identification of viral resistance to β-D-2′-CH₃-riboC in the patientcan be determined by detecting the presence of cytidine at nucleotide1214 of the RNA polymerase region of BVDV or cytidine at nucleotide 8443of HCV.

In one embodiment, the present invention includes a method for treatinga patient infected with Flaviviridae comprising:

-   -   (i) administering an effective amount of β-D-2′-CH₃-riboC or a        prodrug, such as the 3′ valine ester prodrug of        β-D-2′-CH₃-riboC, or a pharmaceutically acceptable salt thereof;    -   (ii) obtaining a viral culture sample from the patient;    -   (iii) culturing the sample and comparing the plaque growth        between the sample and wild type virus;    -   (iv) determining whether the plaque growth of the sample is        smaller than the plaque growth of the wildtype, which indicates        resistance to β-D-2′-CH₃-riboC;    -   (v) administering an effective amount of interferon to those        patients that are resistant to β-D-2′-CH₃-riboC.

In another embodiment, the invention provides a method for treating apatient infected with Flaviviridae comprising:

-   -   (i) administering an effective amount of β-D-2′-CH₃-riboC or a        prodrug, such as the 3′ valine ester prodrug of        β-D-2′-CH₃-riboC, or a pharmaceutically acceptable salt thereof;    -   (ii) obtaining a viral sample from the patient;    -   (iii) determining the replication fitness of the viral;    -   (iv) determining whether the replication fitness of the sample        is less than the replication fitness of the wild-type virus,        which indicates resistance to β-D-2% CH₃-riboC;    -   (v) administering an effective amount of interferon to those        patients that are resistant to β-D-2′-CH₃-riboC.

In one embodiment, viral plaque growth and/or viral replication fitnesscan be quantitated by a viral plaque assay. In other embodiments, otherassays, such as the infectious center assay, virus-inducible reporterassay, transformation assay, end point dilution assay, or RT-PCRtechnology can be used to quantitate viral titers (Flint et al.Principles of Virology (ASM) Chapter 2; Wagner & Hewlett. Basic Virology(Blackwell), Chapters 9 & 10).

A plaque assay can be conducted to quantitate viral plaque growth and/orreplication fitness. A dilute solution of the virus can be applied to aculture dish that contains a monolayer of host cells. The cells can beoverlayed with a semisolid layer (such as a viscous medium, for example,agar) to prevent virus diffusion from one infected cell to another.After incubation the ‘plaques’ can be recognized, and the number ofinfective virus particles in the original suspension estimated. Onemethod to recognize the plaques is through the use of antibody stainingmethods to detect viral antigens within infected cells in the monolayer.These infected cells can then be visualized using a chromagen or afluorescent label on the virus-specific antibody. The plaques can beobserved for phenotypic analysis and/or counted to determine viraltiters. Virus titers can be calculated in focus forming units (FFU)/mL,using the following equation: T_(FFU/mL)=N×5×D; where T is a virus titerin FFU/mL; N is a number of plaques per well; and D is a dilution factorfor the corresponding virus sample. (For example, if 12 plaques werefound in a well corresponding to 10⁻⁵ dilution of virus sample, thanT=12×5×10⁵=6×10⁶ PFU/mL) and viral replication fitness, which is theoverall replicative ability to produce infected progeny in a definedhost environment, can then be determined.

Another aspect of the invention is a method for detecting the presenceof the nucleotide 1214 G to C mutation of the RNA polymerase region ofBVDV (causing a mutation from Serine to Threonine at amino acid 405).Since it is recognized that Ser₄₀₅, the amino acid position of the BVDVputative functional NS5B domain B, is highly conserved among allhepaci-, pesti- and flavivirus genomes (FIG. 11; Lai et al. J Virol.,1999, 73, 10129-36), the corresponding serine residues of the putativefunctional NS5B domain B of other Flaviviridaes that are mutated can bedetected according to the embodiments of the present invention. Forexample, Ser₄₀₅ of the RNA polymerase domain of BVDV corresponds toSer₂₈₂ of the RNA polymerase domain of HCV. Therefore, the embodimentsof the present invention also encompass a G to C mutation of nucleotide8443 of the HCV genome (which corresponds to nucleotide 1214 of the BVDVRNA polymerase region).

In one embodiment, the invention provides a process for detecting amutation that indicates β-D-2′-CH₃-riboC resistance, which includescontacting a sample containing a Flaviviridae nucleic acid sequence withan oligonucleotide probe having a sequence complementary to a section ofthe Flaviviridae genome that includes the mutation; and then determiningif the oligonucleotide hybridizes to the viral nucleic acid.

In other embodiments, the invention provides a method for treating apatient infected with Flaviviridae comprising:

-   -   (i) administering an effective amount of β-D-2′-CH₃-riboC or a        prodrug, such as the 3′ valine ester prodrug of        β-D-2′-CH₃-riboC, or a pharmaceutically acceptable salt thereof;    -   (ii) assaying the blood of the patient to test for        seroconversion from wildtype to mutant virus;    -   (iii) administering an effective amount of interferon.

In yet another embodiment, the invention provides a method for assayinga sample suspected of containing a β-D-2′-CH₃-riboC-resistantFlaviviridae comprising:

-   -   (i) contacting a sample containing a Flaviviridae nucleic acid        sequence with a detectable oligonucleotide probe having a        sequence complementary to the cytidine at nucleotide 1214 of the        RNA polymerase region of BVDV or nucleotide 8443 of the HCV        genome;    -   (ii) allowing the probe to hybridize to the sequence;    -   (iii) detecting the hybridization of the probe to cytidine at        nucleotide 1214 of the RNA polymerase region of BVDV or        nucleotide 8443 of the HCV genome;

In a further embodiment, the invention provides a method for assaying asample suspected of containing a Thr instead of a Ser in the highlyconserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B ofthe RNA polymerase region of a Flaviviridae, which indicates that thevirus is hypersensitive to interferon treatment, comprising:

-   -   (i) contacting a sample suspected of containing a Flaviviridae        nucleic acid sequence with a detectable oligonucleotide probe        having a sequence complementary a codon that encodes Thr in the        position of Ser in the conserved consensus sequence, XRXSGXXXT        (SEQ ID NO: 63), of domain B of the RNA polymerase region of a        Flaviviridae;    -   (ii) allowing the probe to hybridize to the sequence;    -   (iii) detecting the hybridization of the probe to the sequence.

In another embodiment, the invention provides a method for assaying asample suspected of containing a Thr instead of a Ser at amino acidposition 405 or a cytidine at nucleotide 1214 of the RNA polymeraseregion of BVDV, which indicates that the virus is hypersensitive tointerferon treatment, comprising:

-   -   (i) contacting a sample suspected of containing a BVDV nucleic        acid sequence with a detectable oligonucleotide probe having a        sequence complementary to the cytidine at nucleotide 1214 of the        RNA polymerase region;    -   (ii) allowing the probe to hybridize to the sequence;    -   (iii) detecting the hybridization of the probe to cytidine at        nucleotide 1214 of the RNA polymerase region of BVDV.

In another embodiment, the invention provides a method for assaying asample suspected of containing a Thr instead of a Ser in the highlyconserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), of domain B ofthe RNA polymerase region at the highly conserved at amino acid position282 or a cytidine at nucleotide 8433 of the HCV genome, which indicatesthat the virus is hypersensitive to interferon treatment, comprising:

-   -   (i) contacting a sample suspected of containing a HCV nucleic        acid sequence with a detectable oligonucleotide probe having a        sequence complementary to the cytidine at nucleotide 8443;    -   (ii) allowing the probe to hybridize to the sequence;    -   (iii) detecting the hybridization of the probe to cytidine at        nucleotide 8443 of the HCV genome.        Oligonucleotide Probes

Oligonucleotide probes are provided that are capable of detecting thepresence of a 2′-branched pyrimidine nucleoside-induced mutation ofFlaviviridae. The probes are complementary to sequences of viral nucleicacids that include the mutation. These probes can be used in processesand kits. The oligonucleotide probes can detect the nucleotide cytidineat nucleotide 1214 of the RNA polymerase region of BVDV or at nucleotide8443 of the RNA polymerase region of HCV, or other nucleotides ofFlaviviridae that encode the conserved serine of the domain B of RNApolymerase within a Flaviviridae genome (FIG. 11).

The oligonucleotide probes are preferably at least 14 nucleotides inlength, and in a preferred embodiment, are at least 15, 20, 25 or 30nucleotides in length. It is generally not preferred to use a probe thatis greater than approximately 25 or 30 nucleotides in length. In oneembodiment, the oligonucleotide probe can be designed to identify theguanine to cytidine base change at nucleotide 1214 of the RNA polymeraseregion of a BVDV. In another embodiment, the oligonucleotide probe canbe designed to identify the guanine to cytidine base change atnucleotide 8443 of HCV. The oligonucleotide probe can be designed suchthat the mutated region is located in the interior section of thehybridized segment, or alternatively can be on either the 3′ or 5′ endof the hybridized segment. It is preferred that the mutated region belocated near the middle of the probe to allow efficient hybridization.

Table 2 below provides illustrative embodiments of BVDV nucleotidesequences that include nucleotide position 1214 of the RNA polymeraseregion, alternatively referred to as nucleotide position 11,136 (seeGenebank accession number AJ133739; Vassilev and Donis (2000) Virus Res69(2) 95-107). Given these sequences, one of ordinary skill usingstandard algorithms can construct oligonucleotide probes that arecomplementary or substantially complementary to the nucleotide sequencesbelow. The rules for complementary pairing are well known: cytidine(“C”) always pairs with guanine (“G”) and thymine (“T”) or uracil (“U”)always pairs with adenine (“A”). It is recognized that it is notnecessary for the probe to be 100% complementary to the target nucleicacid sequence, as long as the probe sufficiently hybridizes and canrecognize the diagnostic nucleotide. A certain degree of base pairmismatch can generally be tolerated.

TABLE 2 Nonlimiting examples of nucleic acid sequences with a singlepoint mutation at nucleotide 1214 (also referred to as position 11,136:see Genebank accession number AJ133739; Vassilev and Donis, Virus Res2000, 69(2), 95-107) of the RNA polymerase region of BVDV

Therefore, in one embodiment, the oligonucleotide has 1, 2, 3, 4, 5 or 6mismatches in complementarity to the Flaviviridae nucleotide sequence.

Other aspects of the present invention provide a method to treat aFlaviviridae infection by administering a therapeutically effectiveamount of a 2′-branched nucleoside, for example, a 2′-branchedpyrimidine nucleoside, for example β-D-2′-CH₃-riboC, or itspharmaceutically acceptable prodrug and/or salt, to a human in need oftherapy, in combination and/or alternation with one or more drugs thatdirectly or indirectly induce a mutation in a Flaviviridae at a locationother than a mutation of a nucleotide that results in a change fromserine to a threonine in the highly conserved consensus sequence,XRXSGXXXT (SEQ ID NO: 63), of domain B of the RNA polymerase region,and/or one or more drugs that is associated with such mutation. Thecodons ACA, ACG or ACU, which also encode Threonine, can be substitutedfor the codon ACC (in bold) in Table 2 above to detect the presence of aThreonine in domain B of the RNA polymerase region of BVDV.

Another aspect of the present invention provides a method to treatand/or to substantially cure a Flaviviridae infection in a host infectedwith a Flaviviridae that contains a Serine to Threonine mutation in thehighly conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), ofdomain B of the RNA polymerase region by administering a therapeuticallyeffective amount of interferon. Therefore, in other embodiments of thepresent invention, the codons ACA, ACG or ACU, which also encodeThreonine, can be substituted for the codon ACC (in bold) in Table 2above, for example to detect the presence of a Threonine at residue 405of the RNA polymerase region of BVDV.

Table 3 below provides illustrative embodiments of HCV nucleotidesequences that include nucleotide position 8443 of the HCV genome(Genebank accession number AJ238799; Lohmann et al. (1999) Science285(5424)110-113). Nucleotide position 8443 of the HCV genomecorresponds to nucleotide position 11,136 of the BVDV genome andrepresents the conserved Serine residue of the RNA polymerase ofFlaviviridae (Ser₄₀₅ of the BVDV genome, which corresponds to Ser₂₈₂ ofthe HCV genome (see FIG. 11)) that is mutated due to treatment withβ-D-2′-CH₃-riboC. As atated above, given these sequences, one ofordinary skill using standard algorithms can construct oligonucleotideprobes that are complementary or substantially complementary to thenucleotide sequences below.

TABLE 3 Nonlimiting examples of nucleic acid sequences encompassing asingle point mutation at nucleotide 8443 (Genebank accession numberAJ238799; Lohmann et al. (1999) Science 285(5424)110-113) of the RNApolymerase region of HCV

Therefore, in one embodiment, the oligonucleotide has 1, 2, 3, 4, 5 or 6mismatches in complementarity to the Flaviviridae nucleotide sequence.

Other aspects of the present invention provide a method to treat aFlaviviridae infection by administering a therapeutically effectiveamount of a 2′-branched nucleoside, for example, a 2′-branchedpyrimidine nucleoside, for example β-D-2′-CH₃-riboC, or itspharmaceutically acceptable prodrug and/or salt, to a human in need oftherapy, in combination and/or alternation with one or more drugs thatdirectly or indirectly induce a mutation in a Flaviviridae at a locationother than a mutation of a nucleotide that results in a change fromserine to a threonine in the highly conserved consensus sequence,XRXSGXXXT (SEQ ID NO: 63), of domain B of the RNA polymerase region,and/or one or more drugs that is associated with such mutation. Asbefore, the codons ACA, ACG or ACU, which also encode Threonine, can besubstituted for the codon ACC (in bold) in Table 3, for example todetect the presence of a Threonine in domain B of the RNA polymeraseregion of HCV.

Another aspect of the present invention provides a method to treatand/or to substantially cure a Flaviviridae infection in a host infectedwith a Flaviviridae that contains a Serine to Threonine mutation in thehighly conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), ofdomain B of the RNA polymerase region by administering a therapeuticallyeffective amount of interferon. The codons ACA, ACG or ACU, which alsoencode Threonine, can be substituted for the codon ACC (in bold) inTable 3, as above, for example to detect the presence of a Threonine atresidue 282 of the RNA polymerase region of HCV.

In another embodiment, the invention provides an oligonucleotide primerfor amplifying a Flaviviridae nucleic acid sequence. In one embodiment,the oligonucleotide is at least 14 nucleotides in length and hybridizesunder sequence-specific, stringent hybridization conditions to anucleotide sequence that contains the mutation.

Oligonucleotide sequences used as the hybridizing region of a primer canalso be used as the hybridizing region of a probe. Suitability of aprimer sequence for use as a probe depends on the hybridizationcharacteristics of the primer. Similarly, an oligonucleotide used as aprobe can be used as a primer.

It will be apparent to those of skill in the art that, provided withthese embodiments, that specific primers and probes can be prepared by,for example, the addition of nucleotides to either the 5′- or 3′-ends,which nucleotides are complementary to the target sequence or are notcomplementary to the target sequence. So long as primer compositionsserve as a point of initiation for extension on the target sequences,and so long as the primers and probes comprise at least 14 consecutivenucleotides contained within those exemplified embodiments, suchcompositions are within the scope of the invention.

The probe(s) herein can be selected by the following non-limitingcriteria, which are not considered exclusive or determinative: (1) theprobes are selected from the region of the Flaviviridae genome thatcontains the mutation; (2) the probes lack homology with any sequencesof viral genomes that would be expected to compromise the test; and (3)the probes lack secondary structure formation in the amplified nucleicacid that, for example, can interfere with nucleic acid extension by anamplification enzyme such as E. coli DNA polymerase, such as the portionof the DNA polymerase referred to as the Klenow fragment. Prevention ofsecondary structure formation can be accomplished by employing up toabout 15% by weight, preferably 5-10% by weight, dimethyl sulfoxide(DMSO) in the amplification medium and/or increasing the amplificationtemperatures to 30°-40° C.

Further, the probe can have an approximate 50% content of guanine andcytidine, and may not contain multiple consecutive adenine and thymineresidues at the 3′-end of the primer which can result in less stablehybrids.

The probes of the invention can be about 10 to 30 nucleotides long,preferably at least 14, 15, 20, 25, or 30 nucleotides in length. Thenucleotides as used in the present invention can be ribonucleotides,deoxyribonucleotides and modified nucleotides such as inosine ornucleotides containing modified groups that do not essentially altertheir hybridization characteristics. Probe sequences are representedthroughout the specification as single stranded DNA oligonucleotidesfrom the 5′- to the 3′-end. Any of the probes can be used as such, or intheir complementary form, or in their RNA form (wherein T is replaced byU).

The probes according to the invention can be prepared by cloning ofrecombinant plasmids containing inserts including the correspondingnucleotide sequences, optionally by cleaving the latter from the clonedplasmids through the use of adequate nucleases and recovering them, e.g.by fractionation according to molecular weight. The probes according tothe present invention can also be synthesized chemically, for instance,by the conventional phosphotriester or phosphodiester methods orautomated embodiments thereof. In one such automated embodimentdiethylphosphoramidites are used as starting materials and can besynthesized as described by Beaucage et al., Tetrahedron Letters (1981),22:1859-1862. One method for synthesizing oligonucleotides on a modifiedsolid support is described in U.S. Pat. No. 4,458,066. It is alsopossible to use a primer which has been isolated from a biologicalsource (such as a restriction endonuclease digest).

The oligonucleotides used as primers or probes can also comprisenucleotide analogues such as phosphorothiates (Matsukura et al., 1967),alkylphosphorothiates (Miller et al., 1979), peptide nucleic acids(Nielsen et al., 1991; Nielsen et al., 1993), morpholino nucleic acids,locked nucleic acids, pseudocyclic oligonucleobases, 2′-O-4′-C-ethylenebridged nucleic acids or can contain intercalating agents (Asseline etal., 1984).

For designing probes with desired characteristics, the following usefulguidelines known to the person skilled in the art can be applied.Because the extent and specificity of hybridization reactions areaffected by a number of factors, manipulation of one or more of thosefactors will determine the exact sensitivity and specificity of aparticular probe, whether perfectly complementary to its target or not.The importance and effect of various assay conditions, explained furtherherein, are known to those skilled in the art.

The stability of the probe to target nucleic acid hybrid should bechosen to be compatible with the assay conditions. This can beaccomplished by avoiding long AT-rich sequences, by terminating thehybrids with GC base pairs, and by designing the probe with anappropriate T_(m). The beginning and end of the probe should be chosenso that the length and % GC result in a T_(m) of about 2-10° C. higherthan the temperature at which the final assay will be performed. Thebase composition of the probe is significant because G-C base pairsexhibit greater thermal stability due to additional hydrogen bonding ascompared to A-T base pairs. Thus, hybridization involving complementarynucleic acids of higher G-C content will be stable at highertemperatures. Conditions such as ionic strength and incubationtemperature under which the probe will be used should also be taken intoaccount when designing the probe. It is known that hybridization canincrease as the ionic strength of the reaction mixture increases, andthat the thermal stability of the hybrids can increase with increasingionic strength. On the other hand, chemical reagents, such as formamide,urea, DIVISO and alcohols, which disrupt hydrogen bonds, can increasethe stringency of hybridization. Destabilization of hydrogen bonds bysuch reagents can greatly reduce the T_(m). In general, optimalhybridization for synthetic oligonucleotide probes of about 10-50 basesin length occurs approximately 5° C. below the melting temperature for agiven duplex. Incubation at temperatures below the optimum can allowmismatched base sequences to hybridize and can therefore result inreduced specificity. It is desirable to have probes that hybridize onlyunder conditions of high stringency, in which only highly complementarynucleic acid hybrids will form and/or hybrids without a sufficientdegree of complementarity will not form. Accordingly, the stringency ofthe assay conditions determines the degree of complementarity neededbetween two nucleic acid strands that form the hybrid. The degree ofstringency is chosen, for example, to maximize the difference instability between the hybrid formed with the target and the non-targetnucleic acid. In the present case, single base pair changes need to bedetected, which requires conditions of very high stringency.

The length of the target nucleic acid sequence and the length of theprobe sequence should also be considered. In some cases, there can beseveral sequences from a particular region, varying in location andlength, which will yield probes with the desired hybridizationcharacteristics. In other cases, one sequence can be significantlybetter than another which differs merely by a single base.

While it is possible for nucleic acids that are not perfectlycomplementary to hybridize, the longest stretch of perfectlycomplementary base sequences normally will determine hybrid stability.While oligonucleotide probes of different lengths and base compositionscan be used, preferably oligonucleotide probes of this invention arebetween about 14 and 30 bases in length and optionally further have asufficient sequence length that is perfectly complementary to the targetnucleic acid sequence.

Regions in the target DNA or RNA that are known to form strong internalstructures inhibitory to hybridization are less preferred. In oneembodiment, probes with extensive self-complementarity are avoided. Asexplained above, hybridization is the association of two single strandsof complementary nucleic acids to form a hydrogen bonded double strand.It is implicit that if one of the two strands is wholly or partiallyinvolved in a hybrid that it will be less able to participate information of a new hybrid. Intramolecular and intermolecular hybrids maybe formed within the molecules of a single probe if there is sufficientself-complementarity. Such structures can be avoided through carefulprobe design. By designing a probe so that a substantial portion of thesequence of interest is single stranded, the rate and extent ofhybridization can be greatly increased. Computer programs are availableto search for this type of interaction. However, in certain instances,it may not be possible to avoid this type of interaction.

Specific primers and sequence specific oligonucleotide probes can beused in a polymerase chain reaction that enables amplification anddetection of the viral genomic sequences.

One aspect of the invention relates to specific oligonucleotide primers.The invention provides compositions comprising an oligonucleotide primerfor amplifying an Flaviviridae nucleic acid wherein said primer issuitable for amplifying a nucleic acid subsequence from a Flaviviridaemutation. For example, the primer can be capable of detecting a G to Cnucleotide change at nucleotide 1214 of the RNA polymerase region ofBVDV. In another example, the primer can be capable of detecting a G toC nucleotide change at nucleotide 8443 of HCV genome.

Amplification and Detection of a Flaviviridae Mutation

Another aspect of the invention relates to methods for amplifying anddetecting the presence of a Flaviviridae mutation.

DNA or RNA can be extracted from a bodily sample, such as blood ortissue material, such as liver, by a variety of techniques known in theart. An unpure sample, for example samples taken from plasma, serum orblood, can be treated with an amount of a reagent effective to open thecells, fluids, tissues, viral capsids or animal cell membranes of thesample, and to expose and/or separate the strand(s) of the nucleicacid(s), before amplification. This lysing and nucleic acid denaturingstep to expose and separate the strands will allow amplification tooccur much more readily.

In one embodiment, the invention provides a process to detect a mutationwherein a sample suspected of containing Flaviviridae nucleic acidsequence(s) is amplified; the amplified sequence is contacted with anoligonucleotide probe having a sequence complementary to the nucleotidesequence of the mutation; and the sequence is detected by hybridizingthe probe to the sequence. In one embodiment, amplification is achievedby the use of the polymerase chain reaction method. In anotherembodiment, the mutation is a nucleotide change from G to C at position1214 of the RNA polymerase region of the BVDV genome. In yet anotherembodiment, the mutation is a nucleotide change from G to C at position8443 of the HCV genome.

Amplification

The amplification method used can be the polymerase chain reaction (PCR;Saiki et al., 1988), ligase chain reaction (LCR; Landgren et al., 1988;Wu & Wallace, 1989; Barany, 1991), nucleic acid sequence-basedamplification (NASBA; Guatelli et al., 1990; Compton, 1991),transcription-based amplification system (TAS; Kwoh et al., 1989),strand displacement amplification (SDA; Duck, 1990; Walker et al.,1992), amplification by means of Q9 replicase (Lizardi et al., 1988;Lomeli et al., 1989), or any other suitable method to amplify nucleicacid molecules known in the art.

Polymerase Chain Reaction

The PCR process for amplification is generally well known in the art(See, for example, U.S. Pat. Nos. 4,683,202 and 4,683,194). Theamplification process can involve an enzymatic chain reaction forpreparing, in exponential quantities relative to the number of reactionsteps involved, a specific nucleic acid sequence, given that the ends ofthe required sequence are known in sufficient detail thatoligonucleotide primers can be synthesized that will hybridize to them,and that a small amount of the sequence is available to initiate thechain reaction. One primer is complementary to the negative (−) strandand the other is complementary to the positive (+) strand. Annealing theprimers to denatured nucleic acid followed by extension with an enzymesuch as the large fragment of DNA Polymerase I (Klenow) and nucleotidesresults in newly synthesized (+) and (−) strands containing the targetsequence. Because these newly synthesized sequences are also templatesfor the primers, repeated cycles of denaturing, primer annealing andextension results in exponential accumulation of the region defined bythe primer. The product of the chain reaction will be a discrete nucleicacid duplex with termini corresponding to the ends of the specificprimers employed.

Any specific nucleic acid sequence can be produced by the presentprocess. It is only necessary that a sufficient number of bases at bothends of the sequence be known in sufficient detail so that twooligonucleotide primers can be prepared which will hybridize todifferent strands of the desired sequence and at relative positionsalong the sequence such that an extension product synthesized from oneprimer, when it is separated from its template (compliment), can serveas a template for extension of the other primer into a nucleic acid ofdefined length. The greater the knowledge about the bases at both endsof the sequence, the greater can be the specificity of the primers forthe target nuclei acid sequence, and thus the greater the efficiency ofthe process. It will be understood that the word primer as usedhereinafter can refer to more than one primer, particularly in the casewhere there is some ambiguity in the information regarding the terminalsequence(s) of the fragment to be amplified. For instance, in the casewhere a nucleic acid sequence is inferred from protein sequenceinformation a collection of primers containing sequences representingall possible codon variations based on degeneracy of the genetic codecan be used for each strand. One primer from this collection can besubstantially conserved with the end of the desired sequence to beamplified.

A specific nucleic acid sequence is produced by using the diagnosticmarker nucleic acid containing that sequence as a template. If thetarget nucleic acid sequence of the sample contains two strands, it isnecessary to separate the strands of the nucleic acid before they can beused as the template, either as a separate step or simultaneously withthe synthesis of the primer extension products. This strand separationcan be accomplished using any suitable denaturing techniques, includingphysical, chemical or enzymatic means, wherein the word “denaturing”, asused herein, includes all such means. One physical method of separatingthe strands of the nucleic acid involves heating the nucleic acid unituntil it is denatured. Typical heat denaturation can involvetemperatures ranging from about 80-150° C. for times ranging from about1 to 10 minutes. Strand separation can also be induced by an enzyme fromthe class of enzymes known as helicases or the enzyme RecA, which hashelicase activity, and in the presence of riboATP is known to denatureDNA. Reaction conditions suitable for separating the strands of nucleicacids with helicases are described by Kuhn Hoffmann-Berling,CSH-Quantitative Biology, 43:63 (1978), and techniques for using RecAare reviewed in C. Radding, Ann. Rev. Genetics, 16:405-37 (1982).

If the original nucleic acid containing the sequence to be amplified issingle stranded, its compliment is synthesized by adding one or twooligonucleotide primers to it. If an appropriate single primer is added,a primer extension product is synthesized in the presence of the primer,an agent for polymerization, and the four nucleoside triphosphatesdescribed below. The product will be partially complementary to thesingle-stranded nucleic acid and will hybridize with the nucleic acidstrand to form a duplex of unequal length strands that can then beseparated into single strands as described above to produce two singleseparated complementary strands. Alternatively, two appropriate primerscan be added to the single-stranded nucleic acid and the reactioncarried out.

If the original nucleic acid constitutes the sequence to be amplified,the primer extension product(s) produced will be completely orsubstantially completely complementary to the strands of the originalnucleic acid and will hybridize with them to form a duplex of equallength strands to be separated into single-stranded molecules.

When the complementary strands of the nucleic acid or acids areseparated, whether the nucleic acid was originally double or singlestranded, the strands are ready to be used as a template for thesynthesis of additional nucleic acid strands. This synthesis isperformed under conditions allowing hybridization of primers totemplates to occur. Generally it occurs in a buffered aqueous solution,to obtain, for example, a pH range of 7-9. A molar excess (for genomicnucleic acid, usually about 10⁸:1 primer:template) of the twooligonucleotide primers can be added to the buffer containing theseparated template strands. It is understood, however, that the amountof complementary strand cannot be known if the process is used fordiagnostic applications, so that the amount of primer relative to theamount of complementary strand cannot be determined with certainty. As apractical matter, however, the amount of primer added will generally bein molar excess over the amount of complementary strand (template) whenthe sequence to be amplified is contained in a mixture of complicatedlong-chain nucleic acid strands. A large molar excess is preferred toimprove the efficiency of the process.

The deoxyribonucleoside triphosphates dATP, dCTP, dGTP and TTP are alsoadded to the synthesis mixture, either separately or together with theprimers, in adequate amounts and the resulting solution is heated toabout 90-100° C. for from about 1 to 10 minutes, for example from about1 to 4 minutes. After this heating period the solution is allowed tocool to room temperature, which is preferable for the primerhybridization. To the cooled mixture is added an appropriate agent foreffecting the primer extension reaction (called herein “agent forpolymerization”), and the reaction is allowed to occur under conditionsknown in the art. The agent for polymerization can also be addedtogether with the other reagents if it is heat stable. This synthesisreaction can occur from room temperature to a temperature above whichthe agent for polymerization no longer functions. Thus, for example, ifDNA polymerase is used as the agent, the temperature is generally nogreater than about 40° C. Most conveniently the reaction occurs at roomtemperature.

The agent for polymerization can be any compound or system that canfunction to accomplish the synthesis of primer extension products,including enzymes. Suitable enzymes for this purpose include, forexample, E. coli DNA polymerase I, Klenow fragment of E. coli DNApolymerase I, T4 DNA polymerase, other available DNA polymerases,polymerase muteins, reverse transcriptase(s), and other enzymes,including heat-stable enzymes (i.e., those enzymes that perform primerextension after being subjected to temperatures sufficiently elevated tocause denaturation), which can facilitate combination of the nucleosidesin the proper manner to form the primer extension products that arecomplementary to each nucleic acid strand. Generally, the synthesis willbe initiated at the 3′-end of each primer and proceed in the 5′direction along the template strand until synthesis terminates,producing molecules of different lengths. Alternatively, agents forpolymerization that initiate synthesis at the 5′-end and proceed towardthe 3′-end, using the same process as described above, can be used.

The newly synthesized strand and its complementary nucleic acid strandwill form a double-stranded molecule under the hybridizing conditionsdescribed above if the target sequence is present, and this hybrid isused in the succeeding steps of the process. In the next step, thesample treated under hybridizing conditions is subjected to denaturingconditions using any of the procedures described above to providesingle-stranded molecules if the target sequence is present.

New nucleic acid is synthesized on the single-stranded molecules.Additional agents for polymerization, nucleosides and primers can beadded if necessary for the reaction to proceed under the conditionsprescribed above. Again, the synthesis will be initiated at one end ofeach of the oligonucleotide primers and will proceed along the singlestrands of the template to produce additional nucleic acid. After thisstep, half of the extension product will consist of the specific nucleicacid sequence bounded by the two primers.

The steps of denaturing and extension product synthesis can be repeatedas often as needed to amplify the target nucleic acid sequence to theextent necessary for detection. As will be described in further detailbelow, the amount of the specific nucleic acid sequence produced willaccumulate in an exponential fashion.

When it is desired to produce more than one specific nucleic acidsequence from the first nucleic acid or mixture of nucleic acids, anappropriate number of different oligonucleotide primers are utilized.For example, if two different specific nucleic acid sequences are to beproduced, four primers are utilized. Two of the primers are specific forone of the specific nucleic acid sequences and the other two primers arespecific for the second specific nucleic acid sequence. In this manner,each of the two different specific sequences can be producedexponentially by the present process.

The present invention can be performed in a step-wise fashion whereafter each step new reagents are added, or simultaneously or in asingle-step manner, where all reagents are added at the initial step, orpartially step-wise and partially simultaneous, where fresh reagent isadded after a given number of steps. If a method of denaturation, forexample heat, is employed, which can inactivate the agent forpolymerization, as in the case of a heat-labile enzyme, then it isnecessary to replenish the agent after every strand separation step. Thesimultaneous method can be utilized when an enzymatic means is used forthe strand separation step. In the simultaneous procedure, the reactionmixture can contain, in addition to the nucleic acid strand(s) with thedesired sequence, the strand-separating enzyme (e.g., helicase), anappropriate energy source for the strand-separating enzyme (e.g. rATP),the four nucleoside triphosphates, the oligonucleotide primers in molarexcess, and the agent for polymerization (e.g., Klenow fragment of E.coli DNA polymerase I).

If heat is used for denaturation in a simultaneous process, aheat-stable agent such as a thermostable polymerase can be employed thatwill operate at an elevated temperature, for example from about 50-105°C. depending on the agent, at which temperature the nucleic acid willconsist of single and double strands in equilibrium. For smaller lengthsof nucleic acid, lower temperatures of about 40-50° C. can be employed.The upper temperature range will depend on the temperature at which theenzyme will degrade or the temperature above which an insufficient levelof primer hybridization will occur. Such a heat-stable enzyme isdescribed, e.g., by A. S. Kaledin et al., Biokhimiya, 45, 644-651(1980). For this constant temperature reaction to succeed, the primershave their 3′ ends within 6-8 base pairs of each other. Each step of theprocess will occur sequentially notwithstanding the initial presence ofall the reagents. Additional materials can be added as necessary. Afterthe appropriate length of time has passed to produce the desired amountof the specific nucleic acid sequence, the reaction can be halted byinactivating the enzymes in any known manner or by separating thecomponents of the reaction.

The amplification can also be carried out using a temperature-cyclingreaction wherein the temperature is increased incrementally to allow forextension, annealing and denaturation using a heat-stable enzyme.

The process of the present invention can be conducted continuously. Inone embodiment of an automated process, the reaction can be cycledthrough a denaturing region, a reagent addition region, and a reactionregion. In another embodiment, the enzyme used for the synthesis ofprimer extension products can be immobilized in a column. Other reactioncomponents can be continuously circulated by a pump through the columnand a heating coil in series, thus the nucleic acids produced can berepeatedly denatured without inactivating the enzyme.

Flaviviridae genotyping using PCR techniques is commonly known in theart. Further, after PCR has been performed on samples suspected ofcontaining a Flaviviridae, the Flaviviridae genome can be sequenced.

Detection of Hybridization of the Probe and Target Sequence

Suitable assay formats for detecting hybrids formed between probes andtarget nucleic acid sequences in a sample are known in the art (Sambrooket al., 1985). Detection of hybridization can be accomplished whether ornot the nucleic acid has been amplified.

One method of detection is through the use of a labeled probe capable ofhybridizing with the unamplified or amplified nucleic acid sequence anddetermining if the probe has hybridized. Such probe necessarily containsthe nucleotide that is suspected of being mutated, such as 1214 of theRNA polymerase of BVDV or nucleotide 8443 of the HCV genome.

Oligonucleotides can be labeled by incorporating a label detectable byspectroscopic, photochemical, biochemical, immunochemical, or chemicalmeans. Useful labels include ³²P, fluorescent dyes, electron-densereagents, enzymes (as commonly used in ELISAs), biotin, or haptens andproteins for which antisera or monoclonal antibodies are available.

The nucleic acid can be detected by analyzing it by Northern or Southernblots with or without radioactive probes. In one embodiment, a smallsample of DNA from, e.g., peripheral blood suspected of containingFlaviviridae, is analyzed via a Southern blot technique usingoligonucleotide probes to detect the specific nucleic acid viral marker.In another embodiment, a small sample of DNA from, e.g., peripheralblood suspected of containing Flaviviridae, is first amplified and thenanalyzed via a Southern blot technique using oligonucleotide probes todetect the specific nucleic acid viral marker.

Another method involves the oligomer restriction technique (such asdescribed in U.S. Pat. No. 4,683,194). In this procedure, an amplifiednucleic acid is denatured and hybridized in solution to a labeledoligonucleotide probe which hybridizes specifically to the targetsequence (i.e., spans the particular conserved region contained by theprimers) and spans at least one restriction site of interest. The duplexformed between target and probe will reconstitute the restriction site,and when cleaved with restriction enzyme, such as, e.g., BglI, PvuII, orHifI, releases a labeled probe fragment which can be resolved from thefull-length probe by gel electrophoresis. The resulting gel is thenautoradiographed. Analysis of the amplified product by this method canbe rapid, i.e., within a few hours.

Another method that can be used to analyze an amplified product is thedot blot method. In a dot-blot method, amplified target DNA isimmobilized on a solid support, such as a nylon membrane. Themembrane-target complex is incubated with labeled probe under suitablehybridization conditions, unhybridized probe is removed by washing undersuitably stringent conditions, and the membrane is monitored for thepresence of bound probe.

An alternate format is a “reverse” dot-blot format, in which anamplified target DNA is labeled and the probes are immobilized on asolid support, such as a nylon membrane (see Saiki et al., 1989, Proc.Natl. Acad. Sci. USA 86:6230, and PCT Patent Publication No. 89/11548).The target DNA is typically labeled during amplification by theincorporation of one or more labeled primers. One or both of the primerscan be labeled. The membrane-probe complex is incubated with the labeledamplified target DNA under suitable hybridization conditions,unhybridized target DNA is removed by washing under suitably stringentconditions, and the filter is then monitored for the presence of boundtarget DNA.

Alternatively, the reverse dot-blot assay can be carried out using asolid support having a plurality of probe hybridization sites or wells.For example, a microwell plate is particularly useful in large scaleclinical applications of the present methods. Probes can be immobilizedto a microwell plate either by passive binding or through a proteinintermediate, such as bovine serum albumin (BSA), which adheres tomicrowell plates. Reverse dot-blot methods carried out in a microwellplate are described in U.S. Pat. No. 5,232,829, and Loeffelholz et al,1992, J. Clin. Microbiol. 30(11):2847-2851. In another embodiment of theinvention, a reverse dot-blot assay is carried out using microwellplates, and the primers are labeled with biotin, as described inLevenson and Chang, 1989, in PCR Protocols: A Guide to Methods andApplications, (Innis et al., eds., Academic Press. San Diego) pages99-112. The probes are conjugated with BSA (see Tung et al., 1991,Bioconjugate Chem. 2:464-465, incorporated herein by reference) andimmobilized on a microwell plate. Following amplification using thelabeled primers and hybridization with the immobilized probes, theamplified nucleic acid is detected by first binding the biotin toavidin-horseradish peroxidase (A-HRP) or streptavidin-horseradishperoxidase (SAHRP), which is then detected by carrying out a reaction inwhich the HRP catalyzes a color change of a chromogen.

In an alternative method of immobilizing hybridization duplexes fordetection, BSA-conjugated probes are bound to magnetic microparticles.The bound probes are hybridized in solution to labeled amplificationproduct. Following hybridization, probe-target duplexes are removed fromthe solution magnetically, and the magnetically immobilizedhybridization duplexes are then detected.

Another method of detection is referred to as a 5′-nuclease assay inwhich the labeled detection probes are added during the PCRamplification process. The probes are modified so as to prevent themfrom acting as primers for DNA synthesis. Any probe which hybridizes totarget DNA during each synthesis step, i.e., during primer extension, isdegraded by the 5′ to 3′ exonuclease activity of the DNA polymerase,e.g., Taq DNA polymerase. The degradation product from the probe is thendetected. Thus, the presence of probe breakdown product indicates boththat hybridization between probe and target DNA occurred and that theamplification reaction occurred. See also for example, U.S. Pat. No.5,210,015.

The assay formats described above typically utilize labeledoligonucleotides to facilitate detection of the hybrid duplexes.Oligonucleotides can be labeled by any of the previously mentionedtechniques, such as incorporating a label detectable by spectroscopic,photochemical, biochemical, immunochemical, or chemical means. Usefullabels include ³²P, fluorescent dyes, electron-dense reagents, enzymes(as commonly used in ELISAS), biotin, or haptens and proteins for whichantisera or monoclonal antibodies are available.

An alternative method for detecting the amplification of a Flaviviridaenucleic acid is by monitoring the increase in the total amount ofdouble-stranded DNA in the reaction mixture (as described in Higuchi etal., 1992, Bio/Technology 10:413-417; Higuchi et al., 1993,Bio/Technology 11:1026-1030; and European Patent Publication Nos.487,218 and 512,334). The detection of double-stranded target DNA relieson the increased fluorescence that ethidium bromide (EtBr) and other DNAbinding labels exhibit when bound to double-stranded DNA. The increaseof double-stranded DNA resulting from the synthesis of target sequencesresults in a detectable increase in fluorescence.

Yet another method useful for detecting Flaviviridae mutations isthrough reverse hybridization assays. This is especially useful if amultitude of probes are involved. In one embodiment the selected set ofprobes are immobilized to a solid support in known distinct locations(dots, lines or other figures). In another embodiment the selected setof probes can be immobilized to a membrane strip in a line fashion. Saidprobes can be immobilized individually or as mixtures to delineatedlocations on the solid support. In a specific embodiment, a line probeassay can be used to screen for Flaviviridae genotypes containing themutation of the present invention. The line probe assay involvesmultiple probes that are immobilized in parallel lines on a membrane,then a reverse hybridization of amplified nucleic acid fragments isperformed. The hybrid can then be detected via a biotin-streptavidincoupling with a non-radioactive color developing system. See, forexample, WO 97/40193.

Flaviviridae genotyping techniques can also be used to analyze thepresence of Flaviviridae mutations. For example, sequence basedphylogenetic analysis, differential hybridization, PCR or fragmentlength polymorphism can be used.

Detection of Flaviviridae Protein/Peptide Markers

In another embodiment, the invention provides a process for detectingviral markers diagnostic for long term 2′-branched nucleoside therapyfailure for Flaviviridae infection wherein a sample containingFlaviviridae protein, peptides, or peptide fragments is analyzed forsuch viral markers. The proteins, peptides, or peptide fragmentscorrelated with therapy failure can be detected by any generallyapplicable protein detection technology known in the art, includingwestern blot, two dimensional gel electrophoresis, enzyme linkedimmunosorbent assays (ELISA), enhanced chemiluminescence (ECL),immunohistochemistry, ELI-Spot assays, peptide sequencing, or antibodybased protein array technology. For example, protein expression ofFlaviviridae viral markers diagnostic for 2′-branched nucleosidetreatment can be analyzed with classical immunohistological methods. Inthese, the specific recognition is provided by the primary antibody(polyclonal or monoclonal) to the specific viral marker, but thesecondary detection system can utilize fluorescent, enzyme, or otherconjugated secondary antibodies. As a result, an immunohistologicalstaining of the Flaviviridae infected tissue section for pathologicalexamination is obtained.

Another method for detecting proteins, peptides, or peptide fragmentsthat are diagnostic for long term response of Flaviviridae carriers to2′-branched nucleoside therapy is the western blot. In brief, a samplecontaining Flaviviridae protein, peptide, or peptide fragments isseparated via means of an electrophoretic gel. The separated proteinsare then transferred to a medium such as nitrocellulose. Antibodieshaving a detectable label such as streptavidin-alkaline phosphatasereactive to specific Flaviviridae amino acid sequences correlated to2′-branched nucleoside failure are then contacted onto thenitrocellulose medium containing the Flaviviridae amino acid sequences.Reactive antibodies will bind with the corresponding Flaviviridae aminoacid sequence, and can be detected using a reagent such as nitobluetetrazolium and 5-bromo-4-chloro-3-indlyl phosphate (BCIP). See, forexample, Jalkanen, M., et al., J. Cell. Biol. 101:976-985 (1985);Jalkanen, M., et al., J. Cell. Biol. 105:3087-3096 (1987).

Alternatively, reactive antibodies present in the sera of Flaviviridaecarriers can be used to detect the presence of Flaviviridae viralmarkers that are diagnostic of 2′-branched nucleoside treatment. Anyknown antibody assay technique known by those skilled in the art,including enzyme immunoassay (EIA), can be used. For example, in oneembodiment a sample from an Flaviviridae carrier containing Flaviviridaespecific antibodies is contacted with a solid support array containingspecific Flaviviridae peptides correlated with 2′-branched nucleosidetherapy success and/or failure. The reactive antibodies are thendetected using rabbit anti-human IgG antibodies labeled withstreptavidin-alkaline phosphatase and a reagent containing exposed tonitoblue tetrazolium and 5-bromo-4-chloro-3-indlyl phosphate.

Another method for detecting proteins, peptides, or peptide fragmentsthat are diagnostic for long term response of Flaviviridae carriers to2′-branched nucleoside therapy is by sequencing the protein, peptide, orpeptide fragment using techniques known to one of ordinary skill in theart (see, for example, Matsudaira, P., J Biol Chem 262: 10035-10038,(1987); Salinovich, O. and Montelano, R., Anal. Biochem. 156: 341,(1986); Tarr, G. E.: Manual Edman Sequencing System. In: Shively, J. E.,(ed.) Methods of Protein Microcharacterization. The Humana Press Inc.,Clifton, N.J., 1986, pp. 155-194; and Fernandez, J., Andrews, L. andMische, S., Anal. Biochem. 218: 112-117, (1994)). For example, one coulduse the Edman technique to determine the amino acid sequence of thepeptide. In brief, the Edman chemistry removes amino acid residues fromthe N-terminus of a protein/peptide, one at a time in sequence. Eachcycle of Edman chemistry, needed for the removal of each amino acidresidue, consists of three steps: a coupling with phenyl isothiocyanate(PITC) under mildly alkaline conditions to form a phenylthiocarbamyl(PTC)-peptide; cleavage to release the first residue as itsanilinothiazolinone (ATZ)-amino acid derivative; conversion of the ATZderivative to a more stable phenylthiohydantoin (PTH)-amino acidderivative. The PTH-amino acid residue, removed in each cycle of Edmandegradation, is identified by small or micro bore RP-HPLC. A fulldescription of the process and possible pitfalls is given by Tarr, G.E.: Manual Edman Sequencing System. In: Shively, J. E., (ed.) Methods ofProtein Microcharacterization. The Humana Press Inc., Clifton, N.J.,1986, pp. 155-194. Alternatively, if a sample yields no N-terminalsequence, the N-terminal residue is blocked, degraded during preparativeprocedures, or for steric reasons unavailable to the Edman chemistryreagents, then the sample can be subjected to controlled specificproteolysis, where the peptides are fractionated and then analyzed. Thisfractionation approach is described by Fernandez, J., Andrews, L. andMische, S.: An improved procedure for enzymatic digestion ofpolyvinylidene difluoride-bound proteins for internal sequence analysis.Anal. Biochem. 218: 112-117, 1994.

Arrays

Another aspect of the present invention provides the use of DNA, RNA orpeptide arrays to detect Flaviviridae nucleic acid viral markers. Sucharrays include DNA macroarrays, DNA microarrays, and DNA microchips. DNAarrays, for example, have been described in U.S. Pat. No. 5,837,832,U.S. Pat. No. 5,807,522, U.S. Pat. No. 6,007,987, U.S. Pat. No.6,110,426, WO 99/05324, 99/05591, WO 00/58516, WO 95/11995, WO95/35505A1, WO 99/42813, JP10503841T2, GR3030430T3, ES2134481T3,EP804731B1, DE69509925C0, CA2192095AA, AU2862995A1, AU709276B2,AT180570, EP 1066506, and AU 2780499. Such arrays can be incorporatedinto computerized methods for analyzing hybridization results when thearrays are contacted with prepared sample nucleotides, for example, asdescribed in PCT Publication WO 99/05574, and U.S. Pat. Nos. 5,754,524;6,228,575; 5,593,839; and 5,856,101. Methods for screening for diseasemarkers are also known to the art, for example, as described in U.S.Pat. Nos. 6,228,586; 6,160,104; 6,083,698; 6,268,398; 6,228,578; and6,265,174. Further descriptions of DNA array methods can, for example befound in: Shoemaker D. D. et al., Nature 409(6822):922-927 (2001); KaneM. D., et al., Nucleic Acids Res 28(22):4552-7 (2000); Taton T A, etal., Science. 289(5485):1757-60 (2000); Jorg Reichert et al., Anal.Chem., 72(24):6025-6029 (2000); Reinke V, Mol Cell 6(3):605-16 (2000);Marx J. Science 289:1670-1672 (2000); Lockhart D. J. et al., Nature405(6788):827-836 (2000); Cortese J. D., The Scientist 14[17]:25 (2000);Cortese J. D., The Scientist 14[11]:26 (2000); Fritz J. et al., Science.288(5464):316-8 (2000); Mark Schena (Ed.), Microarray BiochipTechnology, Eaton Publishing Company, Distributed byTeleChem/arrayit.com; Scherf U., et al., Nat Genet.24(3):236-44 (2000);Ross D. T. et al., Nat Genet. 24(3):227-35 (2000); Walt D. R., Science287: 451-452 (2000); Afshari C. A. et al., Cancer Res 59(19):4759-60(1999); Gwynne P. and Page G., Science, 1999 Aug. 6. (specialadvertising supplement; has a list of microarray-related companies);Baldwin D. et al., Curr Opin Plant Biol 2(2):96-103 (1999); Pollack J.R. et al., Nat Genet 23(1):41-6 (1999); Khan J. et al., Electrophoresis20(2):223-9 (1999); Gerhold D. et al., Trends Biochem Sci 24(5):168-73(1999); Ekins R. and Chu F. W., Trends in Biotechnology 17:217-218(1999); Nuwaysir, E. F. et al., Molecular Carcinogenesis 24:153-159(1999); Sinclair, B. The Scientist, 13(11):18-20 (1999); The ChippingForecast, Nature Genetics (January 1999 Supplement); Schena, M. andDavis, R. W. Genes, Genomes and Chips. In DNA Microarrays: A PracticalApproach (ed. M. Schena), Oxford University Press, Oxford, UK, 1999;Marton M. J. et al., Nat Med. 4(11):1293-301 (1998); Wang D. G. et al.,Science 280(5366):1077-82 (1998); Schena, M. and R. W. Davis. ParallelAnalysis with Biological Chips. in PCR Methods Manual (eds. M. Innis, D.Gelfand, J. Sninsky), Academic Press, San Diego, 1998; Lemieux, B. etal., Molecular Breeding 4:277-289 (1998); Schena, M. et al., Trends inBiotechnology 16:301-306 (1998); Service, R. F., Science282(5388):396-399 (1998); Service, R. F., Science 282(5388):399-401(1998); Kricka, L., Nature Biotechnology 16:513 (1998); Housman, D.,Nature Biotechnology 16(6):492-493 (1998); Ramsay, G., NatureBiotechnology 16(1):40-44 (1998); Marshall, A. et al., NatureBiotechnology 16(1):27-31 (1998); Kononen J. et al., Nat. Med.4(7):844-847 (19998); Blanchard, A. P. (1998) Synthetic DNA Arrays; inGenetic Engineering, Vol. 20, pp. 111-123, edited by J. K. Setlow,Plenum Press, New York; Proudnikov D. et al., Anal Biochem 259(1):34-41(1998); Chen J. J. et al., Genomics 51(3):313-24 (1998); Wallace R. W.,Molecular Medicine Today 3:384-389 (1998); Covacci, A. et al., DrugDevelopment Research 41:180-192 (1997); Forozan, F. et al., Trends inGenetics 13:405-409 (1997); Blanchard, A. P. & L. Hood, NatureBiotechnology 14:1649 (1996); Blanchard, A. P. et al., Biosensors &Bioelectronics 11:687-690 (1996); DeRisi J. et al., Nat Genet14(4):457-60 (1996); Shalon D. et al., Genome Res 6(7):639-45 (1996);Schena M. et al., Proc Natl Acad Sci USA 93(20):10614-9 (1996); andSchena M. et al., Science 270(5235):467-70 (1995).

Probes on an array can be of varying lengths, including, but not limitedto, as short as about 10-30 nucleotides long or as long as an entireFlaviviridae gene or Flaviviridae clone, which can be up to severalkilobases. In addition, sequences of the various lengths as thosedescribed in Tables 2 and 3 (Seq ID Nos. 1-62) can be used as probes.The array can be designed such that all probes on the array canhybridize to their corresponding genes at about the same hybridizationstringency. Probes for arrays should be unique at the hybridizationstringencies used. A unique probe is only able to hybridize with onetype of nucleic acid per target. A probe is not unique if at thehybridization stringency used, it hybridizes with nucleic acids derivedfrom two different genes, i.e. related genes, or non-homologoussequences. The homology of the sequence of the probe to the gene and thehybridization stringency used help determine whether a probe is uniquewhen testing a selected sample. Probes also may not hybridize withdifferent nucleic acids derived from the same gene, i.e., splicevariants. Since the splice variants of interest are known, severaldifferent probe sequences can be chosen from the target gene sequence ofinterest for an array, such that each probe can only hybridize tonucleic acid derived from one of the splice variants. In one embodiment,arrays containing Seq ID Nos. 1-62 are used at hybridization conditionsallowing for selective hybridization. At conditions of selectivehybridization, probes hybridize with nucleic acid from only oneidentified sequence. At conditions of selective hybridization, probeshybridize with nucleic acid from only one identified sequence. Inanother embodiment, arrays containing any Flaviviridae sequence ofinterest are used at hybridization conditions allowing for selectivehybridization. At conditions of selective hybridization, probeshybridize with nucleic acid from only one identified sequence.

In one embodiment, the use of the microarray first requiresamplification of genes of interest, such as by reverse transcription ofmRNA or total RNA followed by polymerase chain reaction using methodsknown in the art. As the nucleic acid is copied, it is tagged with alabel that can be used in the detection and quantitation methods knownin the art. The nucleic acid can be labeled with radioactive ornon-radioactive labels, but preferably contain fluorescent labels. Thelabeled nucleic acid is introduced to the microarray containing thesequence probes of interest and allowed to react for a period of time.Thereafter, the substrate is washed free of extraneous materials,leaving the nucleic acids on the target bound to the fixed probemolecules allowing for detection and quantitation by methods known inthe art such as by autoradiograph, liquid scintillation counting, and/orfluorescence. As improvements are made in hybridization and detectiontechniques, they can be readily applied by one of ordinary skill in theart. As is well known in the art, if the probe molecules and targetmolecules hybridize by forming a strong non-covalent bond between thetwo molecules, it can be reasonably assumed that the probe and targetnucleic acid are essentially completely complementary if the annealingand washing steps are carried out under conditions of high stringency.The detectable label provides a means for determining whetherhybridization has occurred. By obtaining an image of the array with adetection and quantitation method known in the art such asautoradiography, liquid scintillation counting, or fluorescence it canbe determined if and to what extent Flaviviridae gene sequences arepresent, by comparing intensities at specific locations on the array.High quantitation signals indicate that a particular sequence is presentin a prepared sample, and an absent quantitation signal shows that aparticular sequence is not present. The presence of various genesequences under different conditions can be directly compared, such asprior to 2′-branched nucleoside treatment and during 2′-branchednucleoside treatment. Similarly, it can be determined what sequences arepresent in response to certain stimuli such as a 2′-branched nucleoside.

In one embodiment, the Flaviviridae sequence profile of a patient can betracked over time using DNA array technologies. In an alternativeembodiment, a patient with Flaviviridae receiving 2′-branched nucleosideas a modality, or other anti-Flaviviridae modality, can be monitored,over time, for changes in the aforementioned Flaviviridae genomicsequences in response to the treatment.

Arrays containing Seq ID Nos. 1-62, or any other identified Flaviviridaesequence of interest, can be made by any array synthesis method known inthe art, such as spotting technology or solid phase synthesis viaphotolithography. Arrays can also be printed on solid substrates, e.g.,glass microscope slides. Before printing, slides are prepared to providea substrate for binding, as known in the art. Arrays can be printedusing any printing techniques and machines known in the art. Printinginvolves placing the probes on the substrate, attaching the probes tothe substrate, and blocking the substrate to prevent non-specifichybridization, as known in the art. Preferably the arrays of thisinvention are synthesized by solid phase synthesis using a combinationof photolithography and combinatorial chemistry. Some of the keyelements of probe selection and array design are common to theproduction of all arrays. Strategies to optimize probe hybridization,for example, are invariably included in the process of probe selection.Hybridization under particular pH, salt, and temperature conditions canbe optimized by taking into account melting temperatures and by usingempirical rules that correlate with desired hybridization behaviors (asdescribed in Keller, G. H., and M. M. Manak (1987) DNA Probes, StocktonPress, New York, N.Y., pp. 169-170, hereby incorporated by reference).Computer models can be used for predicting the intensity andconcentration-dependence of probe hybridization.

Moderate to high stringency conditions for hybridization are known inthe art. An example of high stringency conditions for a blot arehybridizing at 68° C. in 5×SSC/5×Denhardt's solution/0.1% SDS, andwashing in 0.2×SSC/0.1% SDS at room temperature. An example ofconditions of moderate stringency are hybridizing at 68° C. in5×SSC/5×Denhardt's solution/0.1% SDS and washing at 42° C. in 3×SSC. Theparameters of temperature and salt concentration can be varied toachieve the desired level of sequence identity between a probe and atarget nucleic acid. See, for example, Ausubel et al. (1995) CurrentProtocols in Molecular Biology, John Wiley & Sons, NY, N.Y., for furtherguidance on hybridization conditions. The melting temperature isdescribed by the following formula (Beltz, G. A. et al., [1983] Methodsof Enzymology, R. Wu, L. Grossman and K. Moldave [Eds.] Academic Press,New York 100:266-285). Tm=81.5° C.+16.6 Log [Na+]+0.41(+G+C)−0.61(%formamide)−600/length of duplex in base pairs.

Nucleic acids useful in this invention can be created by PolymeraseChain Reaction (PCR) amplification. PCR products can be confirmed byagarose gel electrophoresis. PCR is a repetitive, enzymatic, primedsynthesis of a nucleic acid sequence. This procedure is well known andcommonly used by those skilled in this art (see, for example, Mullis,U.S. Pat. Nos. 4,683,195, 4,683,202, and 4,800,159; Saiki et al.,Science 230:1350-1354 (1985)). PCR is used to enzymatically amplify aDNA fragment of interest that is flanked by two oligonucleotide primersthat hybridize to opposite strands of the target sequence. The primersare oriented with the 3′-ends pointing towards each other. Repeatedcycles of heat denaturation of the template, annealing of the primers totheir complementary sequences, and extension of the annealed primerswith a DNA polymerase result in the amplification of the segment definedby the 5′-ends of the PCR primers. Since the extension product of eachprimer can serve as a template for the other primer, each cycleessentially doubles the amount of DNA template produced in the previouscycle. This results in the exponential accumulation of the specifictarget fragment, up to several million-fold in a few hours. By using athermostable DNA polymerase such as the Taq polymerase, which isisolated from the thermophilic bacterium Thermus aquaticus, theamplification process can be completely automated. Other enzymes thatcan be used are known to those skilled in the art.

Alternatively, probes made of peptide nucleic acids (PNAs) can be usedas substitutes for probes made of oligonucleotides for the same uses asdescribed above. The substitution of PNAs for oligonucleotides is wellknown in the art: The synthesis of peptide nucleic acids via preformedmonomers has been described, for example, in PCT patent applications WO92/20702 and WO 92/20703. Recent advances have also been reported on thesynthesis, structure, biological properties, and uses of PNAs. See, forexample, PCT Patent application WO 93/12129, U.S. Pat. No. 6,617,422 toNeilsen P. E. et al., U.S. Pat. No. 5,539,083 to Cook et al., U.S.Patent application US20030059789A1, U.S. Pat. No. 6,475,721 to Kleiberet al., Egholm et al., Nature:365, 566-568 (1993), Nielsen et al.,Science 254:1497-1500 (1991); and Egholm et al., J. Am. Chem. Soc.,114:1895-1897 (1992).

Kits

A suitable test kit for use in an assay to determine the resistancestatus of a Flaviviridae sample to 2′-Branched nucleoside which makesuse of a methodology according to one aspect of the invention, comprises(1) an oligonucleotide being complementary to a region of the wild-typeDNA sequence (or its corresponding RNA) or to a region of the mutant DNAsequence as described herein; (2) materials required for polymerizationof the nucleic acid from the 3′-end of the oligonucleotide; and (3) ameans for determining the presence of an oligonucleotide primer extendedproduct. Polymerization materials include appropriate enzymes, buffers,washing solutions, labels and substrates for the label, if necessary. IfPCR is used to amplify nucleic acid then additional materials such asappropriate oligonucleotide primers that will amplify a region of thewild-type DNA sequence (or its corresponding RNA) or a region of themutant DNA sequence as described herein (or its corresponding RNA) anddNTP's (deoxynucleoside triphosphates) should be included. Instructionsfor conducting the assay can also be included.

A suitable test kit for use in an assay to determine the sensitivity ofa Flaviviridae sample to interferon which makes use of a methodologyaccording to another aspect of the invention comprises anoligonucleotide being complementary to a region of the wild-type DNAsequence (or its corresponding RNA) or to the pertinent region of themutant DNA sequence, along with materials required to permithybridization. Such materials include appropriate buffers, washingsolutions, labels, and substrates for the labels, if necessary. In oneembodiment, the oligonucleotide is labeled. If PCR is used to amplifynucleic acid prior to hybridisation then additional materials such asappropriate oligonucleotide primers that will amplify a region of thewild-type DNA sequence (or its corresponding RNA) or a region of themutant DNA sequence, appropriate enzymes and dNTP's (deoxynucleotidetriphosphates) should be included. Instructions for conducting the assaycan also be included.

In another embodiment, the invention provides a kit for the detection ofa marker of resistance to long term 2′-branched nucleoside treatment ofa Flaviviridae infection. The kit can contain a compartment whichcontains an oligonucleotide probe which binds substantially to a nucleicacid subsequence of the Flaviviridae that contains the diagnosticmarker. Alternatively, the kit contains peptide nucleic acid (PNA) orother antisense mimic probe in substitution for the oligonucleotide. Thekit can also contain reagents to detect the hybridization of the probeto the Flaviviridae nucleic acid viral marker. The present inventionalso includes kits that can contain a primer for the PCR amplificationof Flaviviridae nucleic acids. A kit can also contain a means fordetecting amplified Flaviviridae nucleic acids, such as anoligonucleotide or peptide nucleic acid probe. In some cases, the probeis fixed to an appropriate support membrane. Other optional componentsof the kit include, for example, an agent to catalyze the synthesis ofprimer extension products, the substrate nucleoside triphosphates, meansused to label (for example, an avidin-enzyme conjugate and enzymesubstrate and chromogen if the label is biotin), the appropriate buffersfor PCR or hybridization reactions, and instructions for carrying outthe present method.

In addition, the kit can have a container which includes a positivecontrol containing one or more nucleic acids with a sequence of theFlaviviridae viral genome correlated with therapy failure and/or acontainer including a negative control without such nucleic acids.Moreover, the kit can have a container for a restriction enzyme capableof cleaving a nucleic acid containing the target sequence at a sitecontained in a sequence in the probe.

The invention also provides a kit for the detection and/or geneticanalysis of one or more viral markers of Flaviviridae that arecorrelated with therapy failure that can be present in a biologicalsample comprising the following components: (i) when appropriate, ameans for releasing, isolating or concentrating the nucleic acidspresent in the sample; (ii) when appropriate, at least one suitableprimer pair; (iii) at least two probes as defined above, possibly fixedto a solid support; (iv) a hybridization buffer, or components necessaryfor producing said buffer; (v) a wash solution, or components necessaryfor producing said solution; (vi) when appropriate, a means fordetecting the hybrids resulting from the preceding hybridization; (vii)when appropriate, a means for attaching said probe to a known locationon solid support; and/or (viii) instructions for carrying out thepresent method.

Furthermore, the invention also provides for a kit that contains peptideor peptide fragments corresponding to viral markers correlated with2′-branched nucleoside therapy failure that can be used in animmunoassay to detect the presence of reactive antibodies in a sample.The peptide can be in a stabilized solution or lypholized. Such kit cancontain an appropriate solution for hydrolyzing a lyophilized peptide.The kit can also contain an appropriate solid medium for blotting theaforementioned peptide on. The kit can also contain an appropriatereagent for detecting the presence of reactive antibodies to thepeptide, such as an anti-human IgG antibody labeled withstreptavidin-alkaline phosphatase. Furthermore, the kit can contain adetection agent such as nitoblue tetrazolium and5-bromo-4-chloro-3-indlyl phosphate (BCIP).

Alternatively, the kit can contain antibodies reactive to specificpeptide sequences associated with 2′-branched nucleoside therapy.

IV. Treatment of Flaviviridae Infections

Combination or Alternation Treatment with Anti-Flaviviridae Agents

Drug-resistant variants of Flaviviridae can emerge after prolongedtreatment with an antiviral agent. Drug resistance most typically occursby mutation of a gene that encodes for an enzyme used in viralreplication. The efficacy of a drug against Flaviviridae infection canbe prolonged, augmented, or restored by administering the compound incombination or alternation with a second, and perhaps third, antiviralcompound that induces a different mutation from that caused by theprinciple drug. Combination therapy induces multiple simultaneousstresses on the virus. The pharmacokinetics, biodistribution, or otherparameters of the drug can be altered by such combination or alternationtherapy.

The present invention provides methods to achieve optimal treatment of aFlaviviridae infection through administration of a 2′-branchednucleoside, or a pharmaceutically acceptable prodrug and/or saltthereof, to a human in need of therapy in combination and/or alternationwith one or more drugs that directly or indirectly induce a mutation inthe viral genome at a location other than a mutation of a nucleotidethat results in a change from serine to a different amino acid in thehighly conserved consensus sequence, XRXSGXXXT (SEQ ID NO: 63), ofdomain B of the RNA polymerase region, and/or one or more drugs that isassociated with such mutation.

Interferon Treatment of Mutant Flaviviridae Infections

Another aspect of the present invention provides a method to treatand/or to substantially cure a Flaviviridae infection in a host infectedwith a Flaviviridae that contains a Serine to Threonine mutation at theconserved serine amino acid residue of Domain B of the RNA polymeraseregion of a Flavividae (FIG. 11) by administering a therapeuticallyeffective amount of interferon. In one embodiment, a method is providedto treat and/or to substantially cure a BVDV infection that contains aserine to threonine mutation at amino acid position 405 of the RNApolymerase region by administering a therapeutically effective amount ofinterferon. In another embodiment, a method is provided to treat and/orto substantially cure a HCV infection that contains a serine tothreonine mutation at amino acid position 282 of the RNA polymeraseregion. of HCV by administering a therapeutically effective amount ofinterferon. In a specific embodiment, interferon alpha-2b isadministered to treat and/or to substantially cure the Flaviviridaeinfection.

In a further embodiment, a method is provided to treat and/or tosubstantially cure a Flaviviridae infection in a host suspected of beinginfected with BVDV comprising: (i) obtaining a viral sample from thehost; (ii) identifying whether the Flaviviridae in the sample contains aThreonine at amino acid residue 405 of the RNA polymerase; and (iii)administering an effective amount of interferon to the host infectedwith a Flaviviridae that contains a Serine to Threonine mutation atamino acid 405 of the RNA polymerase region.

In another embodiment, a method is provided to treat and/or tosubstantially cure a Flaviviridae infection in a host suspected of beinginfected with HCV comprising: (i) obtaining a viral sample from thehost; (ii) identifying whether the Flaviviridae in the sample contains aThreonine at amino acid residue 282 of the RNA polymerase; and (iii)administering an effective amount of interferon to the host infectedwith a Flaviviridae that contains a Serine to Threonine mutation atamino acid 282 of the RNA polymerase region.

Interferons include: Intron-A (interferon alpha-2b) by Schering,PEG-INTRON (pegylated interferon alpha-2b) by Schering, Roferon-A(interferon alfa-2a) by Roche, PEGASYS (pegylated interferon alfa-2a) byRoche, INFERGEN (interferon alfacon-1) by InterMune, OMNIFERON (naturalinterferon) by Viragen, ALBUFERON by Human Genome Sciences, REBIF(interferon beta-la) by Ares-Serono, Omega Interferon by BioMedicine,Oral Interferon Alpha by Amarillo Biosciences, and Interferon gamma-1bby InterMune.

Identification of the Serine to Threonine mutation at amino acidposition 405 of the RNA polymerase region of BVDV, or amino acidposition 282 of the RNA polymerase region of HCV, can be accomplished bydetecting the presence of a mutation in the Flaviviridae genome thatwould allow for an amino acid change from Serine to Threonine. In oneembodiment, the presence of cytidine at nucleotide 1214 of the RNApolymerase region of BVDV (where nucleotide 1214 of the RNA polymeraseregion corresponds to nucleotide 11,136 of the BVDV genome) can be usedto detect the amino acid change. In other embodiments, the followingdouble mutations can be detected: 1214 (G to C) and 1215 (C to A); 1214(G to C) and 1215 (C to G); or 1214 (G to C) and 1215 (C to U), whichresult in an amino acid change from serine to threonine at position 405of the RNA polymerase region of BVDV. In another embodiment, thepresence of cytidine at nucleotide 8443 of the HCV genome can be used todetect the amino acid change. In other embodiments, the following doublemutations can be detected: 8443 (G to C) and 8444 (C to A); 8443 (G toC) and 8444 (C to G); or 8443 (G to C) and 8444 (C to U), which resultin an amino acid change from serine to threonine at position 282 of theRNA polymerase region of HCV. The mutations can be detected using any ofthe detection techniques described above, such as labeled probes,reverse hybridization assays, southern blots or any other detectiontechnique known to one skilled in the art.

V. Preparation of Pharmaceutical Compositions

Any host, including a human, exhibiting an infection caused by aFlaviviridae virus can be treated by administering to the patient aneffective amount of a 2′-branched nucleoside or a pharmaceuticallyacceptable prodrug and/or salt thereof, such as β-D-2*-CH₃-riboC or its3′valine ester prodrug, in the presence of a pharmaceutically acceptablecarrier or dilutant, for any of the indications or modes ofadministration as described in detail herein in combination oralternation with a drug that induces a mutation in the viral genome at alocation other than a mutation of a nucleotide that results in a changefrom serine to a different amino acid in the highly conserved consensussequence, XRXSGXXXT (SEQ ID NO: 63), of domain B of the RNA polymeraseregion. The 2′-branched nucleoside, such as β-D-2′-CH₃-riboC, or apharmaceutically acceptable prodrug and/or salt thereof can beadministered alone or in combination or alternation with other antiviralagents as described herein. The active materials can be administered byany appropriate route, for example, orally, parenterally, intravenously,intradermally, subcutaneously, or topically, in liquid or solid form.

A preferred dose of a compound will be in the range from about 1 to 50mg/kg, preferably 1 to 20 mg/kg, of body weight per day, and moregenerally 0.1 to about 100 mg per kilogram body weight of the recipientper day. The effective dosage range of the pharmaceutically acceptablesalts and prodrugs can be calculated based on the weight of the parentnucleoside to be delivered. If the prodrug and/or salt exhibits activityin itself, the effective dosage can be estimated using the weight of theprodrug and/or salt, or by other means known to those skilled in theart.

A compound can be conveniently administered in unit any suitable dosageform, including but not limited to one containing 7 to 3000 mg,preferably 70 to 1400 mg, of active ingredient per unit dosage form. Forexample, an oral dosage of 50-1000 mg of the active ingredient isusually convenient.

Ideally the active ingredient should be administered to achieve peakplasma concentrations of the active compound of from about 0.2 to 70 μM,preferably about 1.0 to 10 μM. This can be achieved, for example, by theintravenous injection of a 0.1 to 5% solution of the active ingredient,optionally in saline, or administered as a bolus of the activeingredient.

The concentration of active compound in the drug composition will dependon absorption, inactivation and excretion rates of the drug as well asother factors known to those of skill in the art. It is to be noted thatdosage values will also vary with the severity of the condition to bealleviated. It is to be further understood that for any particularsubject, specific dosage regimens should be adjusted over time accordingto the individual need and the professional judgment of the personadministering or supervising the administration of the compositions, andthat the concentration ranges set forth herein are exemplary only andare not intended to limit the scope or practice of the claimedcomposition. The active ingredient can be administered at once, or canbe divided into a number of smaller doses to be administered at varyingintervals of time.

A preferred mode of administration of the active compound is oral. Oralcompositions will generally include an inert diluent or an ediblecarrier. They can be enclosed in gelatin capsules or compressed intotablets. For the purpose of oral therapeutic administration, the activecompound can be incorporated with excipients and used in the form oftablets, troches, or capsules. Pharmaceutically compatible bindingagents, and/or adjuvant materials can be included as part of thecomposition.

The tablets, pills, capsules, troches and the like can contain any ofthe following ingredients, or compounds of a similar nature: a bindersuch as microcrystalline cellulose, gum tragacanth or gelatin; anexcipient such as starch or lactose, a disintegrating agent such asalginic acid, Primogel, or corn starch; a lubricant such as magnesiumstearate or Sterotes; a glidant such as colloidal silicon dioxide; asweetening agent such as sucrose or saccharin; or a flavoring agent suchas peppermint, methyl salicylate, or orange flavoring. When the dosageunit form is a capsule, it can contain, in addition to material of theabove type, a liquid carrier such as a fatty oil. In addition, dosageunit forms can contain various other materials which modify the physicalform of the dosage unit, for example, coatings of sugar, shellac, orother enteric agents.

The compound can be administered as a component of an elixir,suspension, syrup, wafer, chewing gum or the like. A syrup can contain,in addition to the active compounds, sucrose as a sweetening agent andcertain preservatives, dyes and colorings and flavors.

The compound, or a pharmaceutically acceptable prodrug and/or saltthereof, can also be mixed with other active materials that do notimpair the desired action, or with materials that supplement the desiredaction, such as antibiotics, antifungals, anti-inflammatories, or otherantivirals, including other nucleoside compounds. Solutions orsuspensions used for parenteral, intradermal, subcutaneous, or topicalapplication can include the following components: a sterile diluent suchas water for injection, saline solution, fixed oils, polyethyleneglycols, glycerine, propylene glycol or other synthetic solvents;antibacterial agents such as benzyl alcohol or methyl parabens;antioxidants such as ascorbic acid or sodium bisulfite; chelating agentssuch as ethylenediaminetetraacetic acid; buffers such as acetates,citrates or phosphates and agents for the adjustment of tonicity such assodium chloride or dextrose. The parental preparation can be enclosed inampoules, disposable syringes or multiple dose vials made of glass orplastic.

If administered intravenously, preferred carriers are physiologicalsaline or phosphate buffered saline (PBS).

In a preferred embodiment, the active compounds are prepared withcarriers that will protect the compound against rapid elimination fromthe body, such as a controlled release formulation, including implantsand microencapsulated delivery systems. Biodegradable, biocompatiblepolymers can be used, such as ethylene vinyl acetate, polyanhydrides,polyglycolic acid, collagen, polyorthoesters and polylactic acid.Methods for preparation of such formulations will be apparent to thoseskilled in the art. The materials can also be obtained commercially fromAlza Corporation.

Liposomal suspensions (including liposomes targeted to infected cellswith monoclonal antibodies to viral antigens) are also preferred aspharmaceutically acceptable carriers. These can be prepared according tomethods known to those skilled in the art, for example, as described inU.S. Pat. No. 4,522,811, which is incorporated herein by reference inits entirety. For example, liposome formulations can be prepared bydissolving appropriate lipid(s), such as stearoyl phosphatidylethanolamine, stearoyl phosphatidyl choline, arachadoyl phosphatidylcholine, and/or cholesterol, in an inorganic solvent that is thenevaporated, leaving behind a thin film of dried lipid on the surface ofthe container. An aqueous solution of the active compound or itsmonophosphate, diphosphate, and/or triphosphate derivatives is thenintroduced into the container. The container is swirled by hand to freelipid material from the sides of the container and to disperse lipidaggregates, thereby forming the liposomal suspension.

The active compound(s) are included in the pharmaceutically acceptablecarrier or diluent in an amount sufficient to deliver to a patient atherapeutically effective amount of compound to inhibit viralreplication in vivo, especially Flaviviridae replication, withoutcausing serious toxic effects in the treated patient. By “inhibitoryamount” is meant an amount of active ingredient sufficient to exert aninhibitory effect as measured by, for example, an assay such as the onesdescribed herein.

Controlled Release Formulations

The field of biodegradable polymers has developed rapidly since thesynthesis and biodegradability of polylactic acid was reported byKulkarni et al., in 1966 (“Polylactic acid for surgical implants,” Arch.Surg., 93:839). Examples of other polymers which have been reported asuseful as a matrix material for delivery devices include polyanhydrides,polyesters such as polyglycolides and polylactide-co-glycolides,polyamino acids such as polylysine, polymers and copolymers ofpolyethylene oxide, acrylic terminated polyethylene oxide, polyamides,polyurethanes, polyorthoesters, polyacrylonitriles, andpolyphosphazenes. See, for example, U.S. Pat. Nos. 4,891,225 and4,906,474 to Langer (polyanhydrides), U.S. Pat. No. 4,767,628 toHutchinson (polylactide, polylactide-co-glycolide acid), and U.S. Pat.No. 4,530,840 to Tice, et al. (polylactide, polyglycolide, andcopolymers). See also U.S. Pat. No. 5,626,863 to Hubbell, et al whichdescribes photopolymerizable biodegradable hydrogels as tissuecontacting materials and controlled release carriers (hydrogels ofpolymerized and crosslinked macromers comprising hydrophilic oligomershaving biodegradable monomeric or oligomeric extensions, which are endcapped monomers or oligomers capable of polymerization andcrosslinking); and WO 97/05185 to Focal, Inc. directed to multiblockbiodegradable hydrogels for use as controlled release agents for drugdelivery and tissue treatment agents.

Degradable materials of biological origin, such as crosslinked gelatin,are well known. Hyaluronic acid has been crosslinked and used as adegradable swelling polymer for biomedical applications (U.S. Pat. No.4,957,744 to Della Valle et. al.; (1991) “Surface modification ofpolymeric biomaterials for reduced thrombogenicity,” Polym. Mater. Sci.Eng., 62:731-735]).

Many dispersion systems are currently in use, or being explored for use,as carriers of substances, and particularly of biologically activecompounds. Dispersion systems used for pharmaceutical and cosmeticformulations can be categorized as either suspensions or emulsions.Suspensions are defined as solid particles ranging in size from a fewmanometers up to hundreds of microns, dispersed in a liquid medium usingsuspending agents. Solid particles include microspheres, microcapsules,and nanospheres. Emulsions are defined as dispersions of one liquid inanother, stabilized by an interfacial film of emulsifiers such assurfactants and lipids. Emulsion formulations include water in oil andoil in water emulsions, multiple emulsions, microemulsions,microdroplets, and liposomes. Microdroplets are unilamellar phospholipidvesicles that consist of a spherical lipid layer with an oil phaseinside, as defined in U.S. Pat. Nos. 4,622,219 and 4,725,442 issued toHaynes. Liposomes are phospholipid vesicles prepared by mixingwater-insoluble polar lipids with an aqueous solution. The unfavorableentropy caused by mixing the insoluble lipid in the water produces ahighly ordered assembly of concentric closed membranes of phospholipidwith entrapped aqueous solution.

U.S. Pat. No. 4,938,763 to Dunn, et al., discloses yet anther method fordrug delivery by forming an implant in situ by dissolving a nonreactive,water insoluble thermoplastic polymer in a biocompatible, water solublesolvent to form a liquid, placing the liquid within the body, andallowing the solvent to dissipate to produce a solid implant. Thepolymer solution can be placed in the body via syringe. The implant canassume the shape of its surrounding cavity. In an alternativeembodiment, the implant is formed from reactive, liquid oligomericpolymers which contain no solvent and which cure in place to formsolids, usually with the addition of a curing catalyst.

A number of patents disclose drug delivery systems that can be used toadminister a 2′-branched nucleoside, or pharmaceutically acceptableprodrug and/or salt thereof, in combination and/or alternation with adrug that induces a mutation in the viral genome at a location otherthan a mutation of a nucleotide that results in a change from serine toa different amino acid in the highly conserved consensus sequence,XRXSGXXXT (SEQ ID NO: 63), of domain B of the RNA polymerase region.U.S. Pat. No. 5,749,847 discloses a method for the delivery ofnucleotides into organisms by electrophoration. U.S. Pat. No. 5,718,921discloses the use of microspheres comprising a polymer and drugdispersed therein as a delivery system. U.S. Pat. No. 5,629,009discloses a delivery system for the controlled release of bioactivefactors. U.S. Pat. No. 5,578,325 discloses the use of nanoparticles andmicroparticles of non-linear hydrophilic hydrophobic multiblockcopolymers for drug delivery. U.S. Pat. No. 5,545,409 discloses adelivery system for the controlled release of bioactive factors. U.S.Pat. No. 5,494,682 discloses the use of ionically cross-linked polymericmicrocapsules as a drug delivery system.

U.S. Pat. No. 5,728,402 to Andrx Pharmaceuticals, Inc. describes acontrolled release formulation that includes an internal phase thatcomprises the active drug, its salt or prodrug, in admixture with ahydrogel forming agent, and an external phase which comprises a coatingthat resists dissolution in the stomach. U.S. Pat. Nos. 5,736,159 and5,558,879 to Andrx Pharmaceuticals, Inc. disclose controlled releaseformulations for drugs with little water solubility in which apassageway is formed in situ. U.S. Pat. No. 5,567,441 to AndrxPharmaceuticals, Inc. discloses a once-a-day controlled releaseformulation. U.S. Pat. No. 5,508,040 discloses a multiparticulatepulsatile drug delivery system. U.S. Pat. No. 5,472,708 discloses apulsatile particle based drug delivery system. U.S. Pat. No. 5,458,888describes a controlled release tablet formulation which can be madeusing a blend having an internal drug containing phase and an externalphase which comprises a polyethylene glycol polymer which has a weightaverage molecular weight of from 3,000 to 10,000. U.S. Pat. No.5,419,917 discloses methods for the modification of the rate of releaseof a drug form a hydrogel which is based on the use of an effectiveamount of a pharmaceutically acceptable ionizable compound that iscapable of providing a substantially zero-order release rate of drugfrom the hydrogel. U.S. Pat. No. 5,458,888 discloses a controlledrelease tablet formulation.

U.S. Pat. No. 5,641,745 to Elan Corporation, plc discloses a controlledrelease pharmaceutical formulation which comprises the active drug in abiodegradable polymer to form microspheres or nanospheres. Thebiodegradable polymer is suitably poly-D,L-lactide or a blend ofpoly-D,L-lactide and poly-D,L-lactide-co-glycolide. U.S. Pat. No.5,616,345 to Elan Corporation plc describes a controlled absorptionformulation for once a day administration that includes the activecompound in association with an organic acid, and a multi-layer membranesurrounding the core and containing a major proportion of apharmaceutically acceptable film-forming, water insoluble syntheticpolymer and a minor proportion of a pharmaceutically acceptablefilm-forming water soluble synthetic polymer. U.S. Pat. No. 5,641,515discloses a controlled release formulation based on biodegradablenanoparticles. U.S. Pat. No. 5,637,320 discloses a controlled absorptionformulation for once a day administration. U.S. Pat. Nos. 5,580,580 and5,540,938 are directed to formulations and their use in the treatment ofneurological diseases. U.S. Pat. No. 5,533,995 is directed to a passivetransdermal device with controlled drug delivery. U.S. Pat. No.5,505,962 describes a controlled release pharmaceutical formulation.

The following examples illustrate various embodiments of the inventionand are not intended to be limiting in any respect.

EXAMPLES Example 1

Isolation β-D-2′-CH₃-riboC-Resistant BVDV

Persistent BVDV infection was established in MDBK cell line (ATCC,Manassas, Va., Catalog #: CCL-22) by in vitro infection of naive cellswith a noncytophatic (ncp) BVDV (strain I-N-dIns; Dr. R. Donis, U. ofNebraska, Lincoln, Nebr.). The multiplicity of infection (MOI) was 0.01.Cells were passaged twice per week (splitting ratio 1:15) until thestable high-level of infection (10⁶-10⁷ focus forming units (FFU) permL) was achieved, as was determined by a focus assay. Next, thepersistently infected cells were grown in 6-well culture plates with 8μM or without β-D-2′-CH₃-riboC (Idenix Pharmaceuticals). Cell cultureswere passaged every three to four days by splitting with a ratio of 1:15to 1:20. After eight passages, cell cultures grown in the presence ofβ-D-2′-CH₃-riboC were expanded to T-75 culture flask, freeze/thawedtwice, and used as a virus stock of β-D-2′-CH₃-riboC-resistant BVDV forfurther characterization. The virus titers in cell cultures weremonitored at the end of each passage by the virus focus assay.

To conduct the virus focus assay, MDBK cells were seeded onto 6-wellplates containing 2×10⁵ cells per well and grown at 37° C./5% CO₂ for atleast 5 hours before use. The test samples (culture supernatantscombined with cell monolayers) were frozen/thawed twice, seriallydiluted by 10-fold in medium, and used to inoculate test cells in 6-wellplates at 0.2 mL per well. The inoculum was removed after 1 hour ofadsorption, and the cells were overlaid with 3 mL of 0.5% agarose incomplete growth medium (1× DMEM (Cellgro), supplemented with 8% horseserum, penicillin, streptomycin, L-glutamine, sodium pyruvate, and 25 mMHEPES). After 3 days of incubation at 37° C./5% CO₂, the plates werefixed for 1 hour with 3 mL of 7.4% formaldehyde in PBS, and washed withPBS. The cell monolayers were permeabilized with 1 mL of PBS-0.25%Triton X-100 per well for 10 minutes, and incubated with 0.5 mL of goatanti-BVDV antiserum (VMDR, Inc.; diluted 1:1000 in PBS-0.25% TritonX-100) for 1 hour. The antiserum was then removed, and cell monolayerswere washed with PBS (twice for 15 min) and incubated with 0.5 mL ofperoxidase-conjugated donkey anti-goat antibody (diluted 1:1000 inPBS-0.25% Triton X-100) for another 1 hour. After the antibody wasremoved, the cell monolayers were washed with PBS (twice for 15 min),and incubated with 0.5 mL of diaminobenzidine (DAB) peroxidase substratesolution (Vector Laboratories) at room temperature until virus focibecome visible (approximately 15 minutes). All incubations were carriedout with rocking. The staining was stopped by washing with water and theplates were allowed to air dry. Virus titers were calculated in FFU/mL,using the following equation: T_(FFU/mL)=N×5×D; where T is a virus titerin FFU/mL; N is a number of foci per well; and D is a dilution factorfor the corresponding virus sample. (For example, if 12 foci were foundin a well corresponding to 10⁻⁵ dilution of virus sample, thanT=12×5×10⁵=6×10⁶ FFU/mL).

Typically, virus titers reached 10⁶-10⁷ FFU/mL after 2-3 passages, anddid not change significantly after further passaging over at least 2months. When such a persistently infected cell line was treated with 8μM β-D-2′-CH₃-riboC, the virus titer declined rapidly and the virus wasno longer detectable after two passages (FIG. 1). However, afteradditional passaging in the presence of the inhibitor, virus reappearedin culture (typically, at passage 3 to 5), and virus titer reachedplateau at 10⁵ FFU/mL, about ten-fold lower than that of untreatedculture (FIG. 1). This 10-fold difference in virus titers was observedeven after 28 days of treatment. This experiment was repeated threetimes and similar results were obtained. The phenotype of the reappearedvirus was remarkably different from the initial wild type virus: ityielded much smaller foci, typically, 3 to 10 times smaller in diameterthen those of the wild type virus (FIG. 2). This phenotype did notchange after prolonged passaging in culture in the presence of theinhibitor for at least 72 days, but, it quickly reverted to the wildtype phenotype (large foci) after the discontinuation of the treatment.

Taken together, these data demonstrate that the wild type virusdisappeared from cell culture after treatment, and theβ-D-2′-CH₃-riboC-resistant virus variant demonstrated lesser replicationfitness in tissue culture.

Example 2

Virus Growth Kinetics

The growth kinetics of both wild type and the β-D-2′-CH₃-riboC-resistantBVDV were compared. MDBK cells were seeded onto 6-well plates (2×10⁵cells per well) and grown at 37° C./5% CO₂ overnight. Cells wereinfected with BVDV I-N-dIns or the β-D-2′-CH₃-riboC-resistant mutant,I-N-dIns β-D-2′-CH₃-riboC-R, at a multiplicity of infection of 0.1.After a 1-hour adsorption, the inoculum was removed, and cells werewashed with PBS and then overlaid with 2 mL of fresh growth medium. ForBVDV I-N-dIns β-D-2′-CH₃-riboC-R, duplicate wells were prepared in thepresence or absence of 8 μM β-D-2′-CH₃-riboC. Cell cultures wereincubated at 37° C./5% CO₂. At 0 (the end of the adsorption period), 6,12, 24, 36, 48, 60, 72 hours post-infection, the cultures werefrozen/thawed twice, and virus titers were quantified by the focus assayas described above.

At 12 hours post-infection, the wild type virus progeny reached asignificant level of over 10⁴ FFU/mL, consistent with the BVDV completelife cycle being 8-14 hours. In contrast, the progeny of the resistantvirus variant was still undetectable at that point (FIG. 3). Thereplication of the resistant virus was first detected at 24 hourspost-infection. At 36 hours post-infection, the replication of theresistant virus was still about 100-fold less efficient than that of thewild type virus. These data clearly demonstrate that theβ-D-2′-CH₃-riboC-resistant BVDV replicates significantly slower than thewild type virus, especially at the early stages of the infection. Thesedata are also consistent with the results presented in FIGS. 1 and 2.

Example 3

Evaluation of the Resistance to β-D-2′-CH₃-riboC

The selected BVDV variant (I-N-dIns β-D-2′-CH₃-riboC-R) is moreresistant to β-D-2′-CH₃-riboC than the wild type BVDV since it canstably replicate to a reasonably high levels in MDBK cells in thepresence of the compound for a long period of time (at least 72 days)without changes in the phenotype nor in the virus titer levels. Toquantitate this resistance, a virus yield reduction assay was performed,using both the wild type and the variant virus.

To conduct the virus yield reduction assay, MDBK cells were seeded onto24-well plates (1×10⁵ cells per well) and grown at 37° C./5% CO₂overnight. Cells were infected with BVDV at a multiplicity of infectionof 0.1. After 1-hour adsorption, the inoculum was removed, and cellswere washed with PBS and then overlaid with 1 mL of fresh growth medium,containing serial 2-fold dilutions of the test compound (0-32 μM forβ-D-2′-CH₃-riboC and 0-800 IU/mL for Intron®A). After incubation at 37°C./5% CO₂ for 48 hours, the plates were frozen/thawed at −70° C. twiceto lyse the cell cultures. The virus titer in the cell culture wasquantified by focus assay as described above. The 50%, 90%, and 4-logeffective concentrations (Mean values±Standard Deviation) for the testcompound were based on duplicate wells. The EC₅₀, EC₉₀ and EC_(4-log)values were derived by curve fitting using XLFit software. The EC₅₀,EC₉₀, and EC_(4 log) are concentrations of test compound, which willreduce viral titer by 50%, 90%, and 99.99%, respectively.

The generation of the infectious wild type BVDV particles was veryefficiently inhibited by β-D-2′-CH₃-riboC, with an EC₅₀ and EC₉₀ valuesof 0.59±0.12 μM and 1.49±0.28 μM, respectively (FIG. 4 and Table 4). Atβ-D-2′-CH₃-riboC concentration of 7.14±1.26 μM the wild type virus yieldwas reduced by 4 logs, and at 16 μM virus titers dropped below thedetection limit (<10 FFU/mL). In contrast, no effect on the resistantvirus yield was observed at the highest β-D-2′-CH₃-riboC concentrationtested (32 μM). Thus, the I-N-dIns β-D-2′-CH₃-riboC-R virus was at least54-fold more resistant to the inhibitor than the wild type virus, basedon the EC₅₀ values obtained by the virus yield reduction assay (>32 μMversus 0.59±0.12 μM).

TABLE 4 Results of BVDV Yield Reduction Assay Compound BVDV strainBiotype¹ EC₅₀ (μM) EC₉₀ (μM) EC_(4 log) (μM) β-D-2′-CH₃-riboC I-N-dInsncp 0.59 ± 0.12 1.49 ± 0.28 7.14 ± 1.26 I-N-dIns β-D-2′- ncp >32 >32 >32 CH₃-riboC-R I-NADL cp 0.68 ± 0.08 1.73 ± 0.11 8.22 ± 0.05 I-NADLS3674T cp >32 >32  >32 IFN I-N-dIns ncp 2.64 ± 1.40  119 ± 34.1 >800I-N-dIns β-D-2′- ncp 0.19 ± 0.04 3.15 ± 0.72 >800 CH₃-riboC-R ¹cp =cytopathic; ncp = noncytopathic

Example 4

Nucleic Acid Sequence Analysis: Identification of the GeneticMutation(s) Responsible for the β-D-2′-CH₃-riboC-Resistant Phenotype.

Based on the nature of the inhibitor, i.e. the nucleoside analog, theviral polymerase was considered as a plausible molecular target. Thus,we begun with the sequencing of the NS5B region for both wild type andthe β-D-2′-CH₃-riboC-resistant BVDV. The viral RNA was extracted fromthe tissue culture lysates after 8 passages of treatment with or withoutβ-D-2′-CH₃-riboC (FIG. 1), the entire NS5B region was subjected to theRT-PCR and sequencing. Viral RNA was extracted from cell cultures usingQIAamp® Viral RNA Mini Kit (QIAGEN) according to the manufacture'sprotocol. The whole NS5B region was transcribed and amplified usingQIAGEN® OneStep RT-PCR Kit. PCR products were purified using QIAquick®PCR Purification Kit (QIAGEN) and sequenced using the ABI PRISM®Sequencing protocol on an automated ABI DNA Sequencer (Perkin-Elmer) atthe Tufts Core Facility, Boston, Mass.

Each region was sequenced in both directions using at least twoindependent RT-PCR products. No mutations were found in the wild typevirus when compared to the previously published sequence of the BVDV(strain I-N-dIns) full-length genome (Vassilev, V. B. and R. O. Donis.(2000) Virus Res. 69 (2): 95-107). Bovine viral diarrhea virus (BVDV)induced apoptosis correlates with increased intracellular viral RNAaccumulation. Only one nucleotide substitution was found in the I-N-dInsβ-D-2′-CH₃-riboC-R virus: 1214G to C, changing amino acid residue Ser toThr at position 405. Interestingly, this amino acid position is locatedto the putative functional NS5B domain B (FIG. 5), identified bymutational analysis (Lai V. C., Kao C. C., Ferrari E., Park J., Uss A.S., Wright-Minogue J., Hong Z., and J. Y. Lau. “Mutational analysis ofbovine viral diarrhea virus RNA-dependent RNA polymerase” J Virol.,1999, 73, 10129-36). This domain is also found in the NS5B region of HCVgenome, as well as in genomes of other flaviviruses. Moreover, the aminoacid position Sen₄₀₅ is highly conserved among all pesti- and flavivirusgenomes.

Example 5

Hypersensitivity to Intron A

Comparison of the wild type I-N-dIns virus and I-N-dInsβ-D-2′-CH₃-riboC-R variant was conducted for their sensitivity to theIntron A in de novo-infected MDBK cells using the virus yield reductionassay, as described above. Again, we found a remarkable differencebetween the two viruses. The wild type virus was moderately inhibited bythe Intron A with an EC₉₀ value of 119±34.1 μM and an approximate 1.5log reduction in virus yield at the highest drug concentration tested(FIG. 6). In contrast, the I-N-dIns β-D-2′-CH₃-riboC-R variant virus wasfound to be much more sensitive to Intron A, with an EC₉₀ value of3.15±0.72 μM and the maximum reduction in the viral yield of nearly 4log (FIG. 6). Based on comparison of the EC₉₀ values, theβ-D-2′-CH₃-riboC-resistant virus was approximately 40 times moresensitive to the Intron A than the wild type BVDV.

Example 6

Combination Treatment with β-D-2′-CH₃-riboC and Intron A

The effect of Intron A, alone or in combination with β-D-2′-CH₃-riboC,on the wild type BVDV was further studied in the persistently infectedMDBK cells. In one experimental setting, the virus titers weredetermined after 7 days (two passages) of single or double treatmentwith several inhibitor concentrations. The results of this experiment,presented in Tables 5A and 5B, and also in FIGS. 7 and 8, can besummarized as follows. β-D-2′-CH₃-riboC alone strongly inhibited BVDV(strain I-N-dIns) propagation in a dose-dependent manner under describedexperimental conditions. Treatment with 8 μM β-D-2′-CH₃-riboC reducedvirus titer 6.2 logs (FIG. 7). Interferon alpha-2b alone had minimalantiviral effect (0.1 log-reduction in virus titers). Single treatmentwith 2 μM β-D-2′-CH₃-riboC or 2000 IU/mL interferon alpha-2b reducedviral titers 1.61 logs and 0.1 log, respectively. The effect of acombination treatment with the same concentrations was 2.22 logs, whichwas 0.51 log higher than the calculated additive effect (1.71 log).Single treatment with 4 μM β-D-2′-CH₃-riboC or 2000 IU/mL interferonalpha-2b reduced viral titers 2.06 logs and 0.1 log, respectively (Table5B, FIG. 8). The effect of a combination treatment with sameconcentrations was 4.56 logs, which was 2.4 logs higher than thecalculated additive effect (2.16 log). Thus, β-D-2′-CH₃-riboC andinterferon alpha-2b acted synergistically to inhibit BVDV, especiallywhen β-D-2′-CH₃-riboC was used at a concentration of 4 μM.

TABLE 5A Effect of β-D-2′-CH₃-riboC and interferon alpha-2b on BVDV(strain I-N-dIns) titers in persistently infected MDBK cells. 0 μM β-D-2 μM β-D- 4 μM β-D- 8 μM β-D- 2′-CH₃- 2′-CH₃- 2′-CH₃- 2′-CH₃- riboCriboC riboC riboC 0 IU/mL 4.03 × 106 ± 1.25 × 105 ± 3.58 × 104 ± 2.50 ×100 ± Interferon alpha-2b 2.34 × 106 3.54 × 104 1.06 × 103 2.89 × 100 5IU/mL 6.44 × 106 ± 2.63 × 105 ± 1.00 × 104 ± 1.25 × 100 ± Interferonalpha-2b 3.15 × 106 7.42 × 104 3.54 × 103 2.50 × 100 50 IU/mL 8.85 × 106± 2.13 × 105 ± 5.75 × 102 ± 0.00 × 100 ± Interferon alpba-2b 4.53 × 1066.72 × 104 4.84 × 102 0.00 × 100 200 IU/mL 5.38 × 106 ± 5.75 × 104 ±2.38 × 102 ± 0.00 × 100 ± Interferon alpha-2b 3.03 × 106 1.32 × 104 2.06× 102 0.00 × 100 1000 IU/mL 2.60 × 106 ± 3.93 × 104 ± 1.34 × 102 ± 0.00× 100 ± Interferon alpha-2b 1.14 × 106 1.80 × 104 2.35 × 102 0.00 × 1002000 IU/mL 3.23 × 106 ± 2.44 × 104 ± 1.12 × 102 ± 0.00 × 100 ±Interferon alpha-2b 1.77 × 106 2.07 × 104 1.93 × 102 0.00 × 100 Numbersrepresent BVDV titer values in FFU/mL.

TABLE 5B Effect of β-D-2′-CH₃-riboC and interferon alpha-2b on BVDV(strain I-N-dIns) titers in persistently infected MDBK cells. 0 μM β-D-2 μM β-D- 4 μM β-D- 8 μM β-D- 2′-CH₃- 2′-CH₃- 2′-CH₃- 2′-CH₃- riboCriboC riboC riboC 0 IU/mL 6.61 5.10 4.55 0.40 Interferon alpha-2b 5IU/mL 6.81 5.42 4.00 0.10 Interferon alpha-2b 50 IU/mL 6.95 5.33 2.760.00 Interferon alpha-2b 200 IU/mL 6.73 4.76 2.38 0.00 Interferonalpha-2b 1000 IU/mL 6.41 4.59 2.13 0.00 Interferon alpha-2b 2000 IU/mL6.51 4.39 2.05 0.00 Interferon alpha-2b Numbers represent log values ofthe BVDV titers.

In another experimental setting, treatment time was extended to 10 daysand the viral titers (strain NY-1) were monitored after each passage(every three to four days). Again, similar synergistic inhibitory effectof β-D-2′-CH₃-riboC and interferon alpha-2b was observed (FIG. 9).Notably, when cell cultures were treated with 8 μM of β-D-2′-CH₃-riboCin combination with 200 IU/mL of Intron A, the virus became undetectableafter 7 days of treatment and did not reappear after further passagingfor at least 27 days. These data are in agreement with our previouslydescribed finding, which is that β-D-2% CH₃-riboC-resistant BVDVvariant, arising after treatment of the persistently infected cells, issensitive to the Intron A. Taken together, these data further suggestthat the resistant virus populations, emerging after treatment of thepersistent virus infection with β-D-2′-CH₃-riboC, can be eliminated bysubsequent treatment with the Intron A.

This invention has been described with reference to specificembodiments. Variations and modifications of the invention, will beobvious to those skilled in the art from the foregoing detaileddescription of the invention.

We claim:
 1. An isolated oligonucleotide probe at least 10 nucleotidesin length that hybridizes to a subsequence of SEQ ID NO:32 comprisingposition 31, wherein the oligonucleotide probe comprises a sequence thatis complementary to the ACC at positions 30 to 32 of SEQ ID NO:32. 2.The probe of claim 1, wherein the oligonucleotide probe has 0, 1, 2, 3,4, 5, or 6 mismatches in complementarity to one of the nucleotidesequences set forth in SEQ ID NOS: 33-62.
 3. A method for identifying adrug resistant hepatitis C virus comprising contacting theoligonucleotide probe of claim 1 with a nucleic acid of said drugresistant hepatitis C virus under conditions wherein said probehybridizes to said nucleic acid, and wherein said drug resistanthepatitis C virus is identified.
 4. The method of claim 3, wherein theviral resistance is to a 2′-branched nucleoside.
 5. The method of claim4, wherein the viral resistance is to a 2′-C-methyl-branched nucleoside.6. A method for identifying a drug resistant hepatitis C viruscomprising contacting the oligonucleotide probe of claim 2 with anucleic acid of said drug resistant hepatitis C virus under conditionswherein said probe hybridizes to said nucleic acid, and wherein saiddrug resistant hepatitis C virus is identified.
 7. The method of claim6, wherein the viral resistance is to a 2′-branched nucleoside.
 8. Themethod of claim 7, wherein the viral resistance is to a2′-C-methyl-branched nucleoside.
 9. An isolated oligonucleotide probe atleast 14 nucleotides in length that hybridizes to a subsequence of SEQID NO:32 comprising position 31, wherein the oligonucleotide probecomprises a sequence that is complementary to the ACC at positions 30 to32 of SEQ ID NO:32.
 10. The probe of claim 9, wherein theoligonucleotide probe has 0, 1, 2, 3, 4, 5, or 6 mismatches incomplementarity to one of the nucleotide sequences set forth in SEQ IDNOS: 33-62.
 11. A method for identifying a drug resistant hepatitis Cvirus comprising contacting the oligonucleotide probe of claim 9 with anucleic acid of said drug resistant hepatitis C virus under conditionswherein said probe hybridizes to said nucleic acid, and wherein saiddrug resistant hepatitis C virus is identified.
 12. The method of claim11, wherein the viral resistance is to a 2′-branched nucleoside.
 13. Themethod of claim 12, wherein the viral resistance is to a2′-C-methyl-branched nucleoside.
 14. A method for identifying a drugresistant hepatitis C virus comprising contacting the oligonucleotideprobe of claim 10 with a nucleic acid of said drug resistant hepatitis Cvirus under conditions wherein said probe hybridizes to said nucleicacid, and wherein said drug resistant hepatitis C virus is identified.15. The method of claim 14, wherein the viral resistance is to a2′-branched nucleoside.
 16. The method of claim 15, wherein the viralresistance is to a 2′-C-methyl-branched nucleoside.
 17. An isolatedoligonucleotide probe about 10 to 30 nucleotides in length thathybridizes to a subsequence of SEQ ID NO:32 comprising position 31,wherein the oligonucleotide probe comprises a sequence that iscomplementary to the ACC at positions 30 to 32 of SEQ ID NO:32.
 18. Theprobe of claim 17, wherein the oligonucleotide probe has 0, 1, 2, 3, 4,5, or 6 mismatches in complementarity to one of the nucleotide sequencesset forth in SEQ ID NOS: 33-62.
 19. A method for identifying a drugresistant hepatitis C virus comprising contacting the oligonucleotideprobe of claim 17 with a nucleic acid of said drug resistant hepatitis Cvirus under conditions wherein said probe hybridizes to said nucleicacid, and wherein said drug resistant hepatitis C virus is identified.20. The method of claim 19, wherein the viral resistance is to a2′-branched nucleoside.
 21. The method of claim 20, wherein the viralresistance is to a 2′-C-methyl-branched nucleoside.
 22. A method foridentifying a drug resistant hepatitis C virus comprising contacting theoligonucleotide probe of claim 18 with a nucleic acid of said drugresistant hepatitis C virus under conditions wherein said probehybridizes to said nucleic acid, and wherein said drug resistanthepatitis C virus is identified.
 23. The method of claim 22, wherein theviral resistance is to a 2′-branched nucleoside.
 24. The method of claim23, wherein the viral resistance is to a 2′-C-methyl-branchednucleoside.